GeneNetwork (GN) provides a scriptable interface that allows other services and web users to retrieve data, map QTLs, generate lists of covariates, or to link to the most appropriate page of data for a particular tissue or transcript. This page documents the GN scriptable interface. GN functions are invoked using commands, which usually takes the form of a URL beginning
+
+
+http://robot.genenetwork.org/webqtl/main.py?...
+
+
At the end of this type of command, after the question mark, you need to add a set of keywords and values separated by the = character, for example, cmd=get or probeset=100011_at. Keywords and values that GN will recognize are listed and explained in the table below.
+
+
+
+
The keyword-value pairs should be separated by the & character. A complete query might look like
+
+cmd=get&probeset=100011_at&probe=all&format=column
+
+
+The order of the keyword-value pairs in the list is unimportant. However, the cmd keyword is required and its value determines what other keywords are required or allowed. In examples, we always use the cmd keyword first.
+
+
+Putting the whole query together results in a string that looks like http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=100011_at&probe=all&format=column
+
+
+Although this command is shown on two lines of text, it is really just one line, and there should be no carriage return or line break.
+
+
+
+
Specific commands
+
+
cmd=genotype retrieves genotype data for any of the supported sets of recombinant inbred lines.
+
+
cmd=get or cmd=trait retrieves trait data from databases of published phenotypes or gene expression data. It can also retrieve marker genotypes as numerical codes for correlation searches.
+
+
+
cmd=map retrieves trait data and searches for associations among BXD marker genotypes, returning marker names, regression coefficients and likelihood ratio statistics.
+
+
cmd=interval retrieves trait data and performs interval mappng, returning map positions of peak likelihood ratio statistic.
+
+
cmd=correlation retrieves trait data and searches for correlations with traits in another
+(or the same) trait database. cmd=correlation and cmd=pearson use Pearson product-moment correlation. cmd=spearman uses Spearman rank-sum correlation.
+
+
+
+
+
+
+
+
+
Commands and Keywords
+
+
+
+
+
+
+
+
+ Function
+
+
+ Command
+ keyword-value
+
+
+ Other keywords
+ (bold keywords are required)
+
+
+ Allowed values
+ [Comments or descriptions in square brackets]
+
pvalue [sorts by ascending
+ pvalue]
+ [sorts by descending correlation by default]
+
+
+
+
+
id
+
yes [Includes NCBI Entrez Gene ID for each transcript in the output (for expression data only).] only [Returns only NCBI Entrez Gene ID for each transcript (for expression data only).]
The script below is used to filter a list of probes or probe sets that target the same gene or transcript to find the single probe or probe set with highest expression and to then display the Statistics Page for that particular data. This script does not use the cgi-bin format.
There are three supported search term types: 1. Gene symbol, 2. RefSeq identifier, 3. Entrez gene identifier. Although not recommended, the string "&searchAlias=1" can be added at the end of the command to retrieve data using the alias of a proper gene symbol when the original does not work. Thus "gene=RP4" will resolve to "gene=Rho" only if you add "&searchAlias=1" at the end of the command.
+ Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
+
A value is required for the probeset but not for probe keyword. With only probeset, commands will retrieve the average for the probeset from different average method. With probeset and probe=all, commands will retrieve data for all probes of that probeset; with probe, data for a single probe. If the specified probeset and probe are inconsistent, no data is returned.
+
+
The Affymetrix cell location code is six characters. The first three characters are the column or x location, and the last three the row or y location; for example, 237198. If the column has less than three digits, it should be preceded by one or two X characters to make three characters. Similarly, the row should be prefixed with one or two Y characters, if necessary; for example, X24YY9 or XX8Y34.
+
+
If chr is omitted, command will retrieve information for all chromosomes.
+
+
If format is omitted, row formatting is the default.
GeneWiki enables you to enrich the annotation of genes. Many of the GeneNetwork (GN) data sets are made up of measruements of mRNA expression levels. User need to be able to incorporate notes and findings related to genes, proteins, and these transcripts. At present, GeneWiki is more of a "note taker" than a true Wiki, although it is possible for you (for better or for worse) to edit notes entered by other users. Please submit or edit a GeneWiki note. The current limitation is 250 letters per entry, although we are likely to increase this significantly. Your entry should be related to a gene, its transcripts, or proteins. When possible include PubMed identifiers and web resource links (URL addresses). Please ensure that the additions will have widespread use.
+
+
Use the "User Code" to enter either your initials or a code for annotations that will allow you to retrieve all genes data of a particular type rapidly.
+
+
To find your GeneWiki entries just preface your search term with "wiki=", for example "wiki=GENSAT" will retrieve all genes that have been annotated with a text that includes "GENSAT" somewhere in the entry.
+
+
Copy the following line to paste into the GeneNetwork entry box:
+86.080 95.164 X 86.054 79.302 78.214 81.756 85.433 89.867 86.466 82.916 69.468 82.407 78.792 X 97.081 75.130 X X 77.937 87.672 84.385 78.359 81.385 92.183 X 91.071 94.072
+
AXB
+
ABF1
3.230
BAF1
24.481
C57BL/6J
40.536
A/J
22.321
AXB1
33.887
AXB2
8.660
+
+
AXB3
5.920
AXB4
23.882
AXB5
51.178
AXB6
32.964
AXB7
57.287
AXB8
X
+
AXB9
2.031
AXB10
41.899
AXB11
30.097
AXB12
13.877
AXB13
17.021
AXB14
23.161
+
+
AXB15
21.279
AXB17
14.422
AXB19
X
AXB21
X
AXB23
45.993
AXB2
45.480
+
+
Copy the following line to paste into the GeneNetwork entry box:
+3.230 24.481 40.536 22.321 33.887 8.660 5.920 23.882 51.178 32.964 57.287 X 2.031 41.899 30.097 13.877 17.021 23.161 21.279 14.422 X X 45.993 45.480
+
+
AXB/BXA
+
ABF1
-13.417
BAF1
-3.256
C57BL/6J
X
A/J
X
AXB1
-27.758
AXB2
10.738
+
AXB3
X
AXB4
49.455
AXB5
X
AXB6
10.560
AXB7
-1.457
AXB8
7.837
+
+
AXB9
2.104
AXB10
3.620
AXB11
X
AXB12
-4.933
AXB13/14
33.413
AXB15
16.036
+
AXB17
X
AXB18/19/20
X
AXB21
-2.955
AXB23
15.773
AXB24
X
BXA1
-9.303
+
+
BXA2
35.737
BXA4
27.019
BXA7
3.783
BXA8/17
X
BXA11
5.131
BXA12
17.545
+
BXA13
X
BXA14
X
BXA16
25.085
BXA18
-12.820
BXA20
26.240
BXA22
-11.779
+
+
BXA23
-10.043
BXA24
3.757
BXA25
13.165
BXA26
11.837
+
+
Copy the following line to paste into the GeneNetwork entry box:
+-13.417 -3.256 X X -27.758 10.738 X 49.455 X 10.560 -1.457 7.837 2.104 3.620 X -4.933 33.413 16.036 X X -2.955 15.773 X -9.303 35.737 27.019 3.783 X 5.131 17.545 X X 25.085 -12.820 26.240 -11.779 -10.043 3.757 13.165 11.837
+
BXA
+
BAF1
55.291
ABF1
68.186
C57BL/6J
43.475
A/J
54.636
BXA1
75.842
BXA2
63.536
+
+
BXA4
X
BXA7
86.283
BXA8
67.661
BXA9
55.820
BXA11
75.330
BXA12
57.127
+
BXA13
78.550
BXA14
60.350
BXA16
X
BXA18
59.133
BXA20
57.704
BXA22
61.872
+
+
BXA23
56.111
BXA24
50.956
BXA25
59.813
BXA26
41.821
+
+
Copy the following line to paste into the GeneNetwork entry box:
Copy the following line to paste into the GeneNetwork entry box:
+6.717 11.511 X 20.201 X 15.175 X 43.132 21.755 47.028 X 22.096 22.219 X X 35.218 49.557 34.263 X 8.783 62.439 40.449 X X 36.554 29.903 28.437 14.894 5.665 60.723 50.458 16.857 37.410 35.857 33.139 42.392 X 62.003 28.797 30.399 X X 30.876 22.120 X 28.619 X 16.156 41.392 30.412 26.209 62.690 23.878 38.629 27.467 23.630 X -0.900 X 43.094 49.670 16.654 21.356 20.465 26.860 29.422 X 30.713 X 25.012 38.874 15.183 25.444 60.408 68.684 X 35.370 34.561 46.055 43.238 72.431 18.648 32.317 45.796 30.291 56.081 X 11.133 52.551 20.704 X 14.143 50.821 32.187 X X X
+
+
BXH
+
+
BHF1
19.365
HBF1
X
C57BL/6J
20.976
C3H/HeJ
18.666
BXH2
16.555
BXH3
X
+
+
BXH4
X
BXH6
19.989
BXH7
18.800
BXH8
17.671
BXH9
15.891
BXH10
X
+
BXH11
22.377
BXH12
15.515
BXH14
13.487
BXH19
22.060
BXH20
X
BXH21
16.232
+
+
BXH22
13.894
B6cC3-1
12.777
+
+
Copy the following line to paste into the GeneNetwork entry box:
+19.365 X 20.976 18.666 16.555 X X 19.989 18.800 17.671 15.891 X 22.377 15.515 13.487 22.060 X 16.232 13.894 12.777
+
CXB
+
CBF1
X
BCF1
84.812
C57BL/6By
53.113
BALB/cBy
84.655
CXB1
52.194
CXB2
82.001
+
+
CXB3
53.063
CXB4
71.660
CXB5
57.900
CXB6
19.980
CXB7
77.547
CXB8
X
+
CXB9
50.419
CXB10
60.208
CXB11
63.764
CXB12
72.970
CXB13
X
+
+
+
Copy the following line to paste into the GeneNetwork entry box:
+X 84.812 53.113 84.655 52.194 82.001 53.063 71.660 57.900 19.980 77.547 X 50.419 60.208 63.764 72.970 X
+
ColXBur
+
ColXBurF1
86.426
BurXColF1
81.796
Col-0
83.611
Bur-0
X
ColXBur2
X
ColXBur3
89.602
+
+
ColXBur4
X
ColXBur5
74.701
ColXBur7
78.680
ColXBur9
102.462
ColXBur10
79.515
ColXBur11
73.302
+
ColXBur12
X
ColXBur13
91.872
ColXBur14
63.728
ColXBur15
79.544
ColXBur16
X
ColXBur17
71.446
+
+
ColXBur19
52.104
ColXBur21
85.598
ColXBur22
87.408
ColXBur24
109.215
ColXBur26
68.489
ColXBur27
69.697
+
ColXBur30
X
ColXBur34
89.146
ColXBur35
60.115
ColXBur36
92.877
ColXBur38
86.557
ColXBur40
X
+
+
ColXBur42
74.984
ColXBur43
85.691
ColXBur44
X
ColXBur45
54.735
ColXBur46
76.603
ColXBur48
104.018
+
ColXBur50
78.257
ColXBur54
75.838
ColXBur56
80.368
ColXBur57
79.908
ColXBur58
81.354
ColXBur59
80.371
+
+
ColXBur60
60.664
ColXBur62
76.757
ColXBur63
69.128
ColXBur64
69.057
ColXBur66
61.558
ColXBur67
98.377
+
ColXBur70
84.559
ColXBur73
72.296
ColXBur75
77.025
ColXBur76
66.074
ColXBur77
X
ColXBur78
91.172
+
+
ColXBur80
80.703
ColXBur81
86.337
ColXBur84
88.624
ColXBur85
115.288
ColXBur86
59.959
ColXBur87
70.448
+
ColXBur89
66.183
ColXBur90
77.485
ColXBur91
61.492
ColXBur93
77.637
ColXBur94
84.862
ColXBur95
70.639
+
+
ColXBur98
85.259
ColXBur99
81.044
ColXBur100
84.771
ColXBur101
76.092
ColXBur102
68.447
ColXBur103
44.485
+
ColXBur104
X
ColXBur105
X
ColXBur107
X
ColXBur108
74.015
ColXBur109
73.675
ColXBur110
X
+
+
ColXBur111
55.311
ColXBur112
78.467
ColXBur113
X
ColXBur114
67.632
ColXBur115
X
ColXBur116
81.590
+
ColXBur117
X
ColXBur119
76.901
ColXBur120
78.602
ColXBur121
X
ColXBur123
88.524
ColXBur126
91.911
+
+
ColXBur128
63.051
ColXBur131
91.851
ColXBur133
85.429
ColXBur135
88.304
ColXBur136
92.845
ColXBur137
74.743
+
ColXBur139
60.406
ColXBur141
92.780
ColXBur143
78.601
ColXBur144
94.333
ColXBur146
X
ColXBur147
70.478
+
+
ColXBur149
86.917
ColXBur150
X
ColXBur151
70.604
ColXBur153
X
ColXBur156
70.762
ColXBur159
88.885
+
ColXBur161
57.360
ColXBur162
90.153
ColXBur163
59.923
ColXBur164
82.626
ColXBur165
77.882
ColXBur166
81.872
+
+
ColXBur167
78.333
ColXBur168
81.740
ColXBur171
76.113
ColXBur172
70.134
ColXBur175
76.452
ColXBur176
88.382
+
ColXBur179
87.972
ColXBur180
64.730
ColXBur181
85.527
ColXBur182
89.301
ColXBur183
X
ColXBur184
64.664
+
+
ColXBur186
77.125
ColXBur188
69.852
ColXBur189
76.279
ColXBur190
93.174
ColXBur191
106.754
ColXBur192
75.470
+
ColXBur193
55.887
ColXBur194
69.538
ColXBur195
74.381
ColXBur196
78.254
ColXBur197
84.384
ColXBur199
X
+
+
ColXBur200
92.910
ColXBur201
72.004
ColXBur202
85.801
ColXBur203
68.790
ColXBur204
86.159
ColXBur206
64.429
+
ColXBur207
51.822
ColXBur209
78.426
ColXBur210
X
ColXBur211
X
ColXBur212
66.453
ColXBur214
49.674
+
+
ColXBur215
87.867
ColXBur220
81.042
ColXBur221
61.831
ColXBur224
80.884
ColXBur225
75.923
ColXBur226
98.168
+
ColXBur227
X
ColXBur228
99.010
ColXBur229
41.371
ColXBur230
81.679
ColXBur231
56.569
ColXBur232
97.273
+
+
ColXBur233
66.921
ColXBur234
X
ColXBur235
X
ColXBur237
X
ColXBur238
56.426
ColXBur240
64.212
+
ColXBur241
85.792
ColXBur243
92.350
ColXBur244
78.642
ColXBur245
67.386
ColXBur246
76.413
ColXBur249
82.843
+
+
ColXBur250
94.898
ColXBur253
69.556
ColXBur254
92.595
ColXBur255
84.117
ColXBur256
84.396
ColXBur258
X
+
ColXBur262
86.408
ColXBur265
86.185
ColXBur267
74.291
ColXBur269
85.267
ColXBur270
73.491
ColXBur272
73.626
+
+
ColXBur274
X
ColXBur275
90.401
ColXBur276
X
ColXBur277
56.693
ColXBur278
X
ColXBur279
86.087
+
ColXBur280
X
ColXBur281
94.440
ColXBur282
83.538
ColXBur284
80.609
ColXBur285
75.760
ColXBur288
81.487
+
+
ColXBur289
90.361
ColXBur290
71.236
ColXBur291
X
ColXBur292
71.223
ColXBur294
72.074
ColXBur296
66.259
+
ColXBur298
X
ColXBur299
67.194
ColXBur300
81.037
ColXBur301
72.476
ColXBur302
86.211
ColXBur303
60.468
+
+
ColXBur304
99.154
ColXBur305
81.872
ColXBur307
89.122
ColXBur308
84.336
ColXBur309
56.036
ColXBur310
85.516
+
ColXBur312
85.638
ColXBur314
72.055
ColXBur315
58.786
ColXBur317
98.698
ColXBur318
X
ColXBur319
X
+
+
ColXBur320
80.609
ColXBur321
65.670
ColXBur322
64.458
ColXBur323
X
ColXBur324
X
ColXBur325
87.841
+
ColXBur326
63.861
ColXBur327
105.495
ColXBur328
73.193
ColXBur329
X
ColXBur332
81.813
ColXBur333
X
+
+
ColXBur335
70.215
ColXBur336
102.559
ColXBur337
65.508
ColXBur338
55.595
ColXBur339
96.415
ColXBur340
65.867
+
ColXBur341
X
ColXBur342
74.449
ColXBur345
X
ColXBur346
95.642
ColXBur347
78.052
ColXBur348
X
+
+
ColXBur351
X
ColXBur352
69.129
ColXBur353
65.478
ColXBur354
68.365
ColXBur355
91.180
ColXBur356
82.515
+
ColXBur357
X
ColXBur358
66.475
ColXBur362
100.399
ColXBur364
93.756
ColXBur365
78.920
ColXBur367
77.854
+
+
ColXBur368
X
ColXBur370
90.768
ColXBur371
55.594
ColXBur372
58.092
ColXBur374
81.057
ColXBur376
86.560
+
ColXBur379
70.603
ColXBur382
43.572
ColXBur383
X
ColXBur384
69.098
ColXBur385
74.397
ColXBur396
77.067
+
+
ColXBur400
79.709
ColXBur402
85.818
ColXBur404
68.245
ColXBur405
81.659
ColXBur406
74.852
ColXBur407
78.159
+
ColXBur409
84.577
ColXBur412
88.073
ColXBur414
65.165
ColXBur419
61.200
ColXBur421
68.541
ColXBur426
106.419
+
+
ColXBur428
X
ColXBur429
69.113
ColXBur430
X
ColXBur431
76.827
ColXBur436
71.710
ColXBur438
X
+
ColXBur440
66.684
ColXBur444
98.421
ColXBur445
96.433
ColXBur446
82.713
ColXBur447
79.530
ColXBur449
75.040
+
+
ColXBur450
85.939
ColXBur451
74.642
ColXBur452
81.053
ColXBur453
X
ColXBur454
81.229
ColXBur455
63.465
+
ColXBur456
72.799
ColXBur457
82.747
ColXBur460
85.203
ColXBur462
59.587
ColXBur463
64.888
ColXBur465
93.933
+
+
ColXBur466
75.853
ColXBur467
57.487
ColXBur468
X
ColXBur470
70.978
ColXBur473
78.393
ColXBur474
63.053
+
ColXBur476
X
ColXBur477
65.184
ColXBur478
80.508
ColXBur479
X
ColXBur482
72.872
ColXBur485
90.816
+
+
ColXBur487
83.841
ColXBur488
77.554
ColXBur489
88.124
ColXBur491
63.410
ColXBur492
61.068
ColXBur494
70.664
+
ColXBur495
83.247
ColXBur496
X
ColXBur497
86.745
ColXBur498
58.285
ColXBur499
X
ColXBur502
86.225
+
+
ColXBur503
75.802
ColXBur504
71.696
ColXBur507
69.241
ColXBur508
71.003
ColXBur509
87.434
ColXBur511
82.439
+
ColXBur513
96.831
ColXBur514
63.159
ColXBur515
75.955
ColXBur516
X
ColXBur517
X
ColXBur518
90.438
+
+
ColXBur519
81.736
ColXBur521
75.447
ColXBur524
67.302
ColXBur525
103.770
ColXBur526
X
ColXBur528
X
+
ColXBur529
83.869
ColXBur530
65.564
ColXBur534
102.949
+
+
+
Copy the following line to paste into the GeneNetwork entry box:
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79.691
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57.455
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80.468
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79.886
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64.920
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56.323
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84.409
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74.449
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HXB/BXH
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HSRBNF1
X
BNHSRF1
110.970
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103.647
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95.829
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81.214
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84.313
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X
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93.835
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HXB13
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76.394
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98.644
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100.860
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104.404
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112.601
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X
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X
HXB22
X
HXB23
X
HXB24
98.467
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HXB25
112.805
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97.550
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98.958
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92.283
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108.442
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86.856
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113.232
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X
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95.615
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105.352
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LXS
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59.080
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46.315
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89.437
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87.309
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49.741
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29.860
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67.335
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104.213
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71.085
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80.798
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58.115
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47.660
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68.383
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57.528
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64.030
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66.204
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X
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94.490
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58.276
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81.920
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75.662
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61.559
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73.410
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89.329
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94.447
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X
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87.750
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69.750
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67.351
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46.252
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X
LXS60
X
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X
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79.158
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62.349
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57.914
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100.818
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69.898
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69.886
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82.810
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83.441
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80.507
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94.317
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78.117
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63.942
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X
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X
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41.933
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63.637
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53.676
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89.219
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X
LXS94
65.297
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X
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88.863
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70.588
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X
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X
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88.272
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71.937
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89.508
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67.748
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X
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76.419
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75.163
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101.519
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44.045
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86.552
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79.804
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+
Copy the following line to paste into the GeneNetwork entry box:
+59.080 46.315 89.437 X 87.309 49.741 29.860 67.335 X 104.213 61.870 71.085 X 80.798 X 58.115 X 64.420 47.660 68.383 57.528 64.030 66.204 X 94.490 X 58.276 81.920 75.662 61.559 73.410 89.329 X 94.447 X X 87.750 69.750 67.351 46.252 X X X 79.158 62.349 57.914 100.818 X 69.898 69.886 82.810 83.441 80.507 94.317 78.117 63.942 X X 41.933 63.637 53.676 89.219 X 65.297 X 88.863 70.588 X X 88.272 71.937 89.508 67.748 X 76.419 75.163 101.519 44.045 86.552 79.804 57.391
+
SXM
+
SMF1
60.066
MSF1
76.919
Steptoe
80.007
Morex
122.832
SM001
85.447
SM002
88.062
+
+
SM003
109.343
SM004
85.448
SM005
93.848
SM006
88.088
SM007
74.384
SM009
X
+
SM010
79.413
SM011
X
SM012
63.176
SM013
67.292
SM014
95.236
SM015
100.175
+
+
SM016
95.854
SM020
85.318
SM021
76.069
SM022
69.545
SM023
101.730
SM024
86.738
+
SM025
104.185
SM027
X
SM030
99.637
SM031
104.924
SM032
91.376
SM035
97.924
+
+
SM039
68.766
SM040
92.028
SM041
78.341
SM042
88.592
SM043
91.877
SM044
69.152
+
SM045
92.461
SM046
71.237
SM048
84.772
SM050
88.102
SM054
88.222
SM055
85.507
+
+
SM056
82.430
SM057
54.067
SM058
103.709
SM059
99.459
SM061
73.284
SM062
112.320
+
SM063
80.569
SM064
61.621
SM065
91.106
SM067
80.536
SM068
98.238
SM069
105.188
+
+
SM070
83.539
SM071
73.012
SM072
65.179
SM073
89.942
SM074
82.730
SM075
81.212
+
SM076
98.461
SM077
X
SM078
92.924
SM079
83.156
SM080
X
SM081
75.906
+
+
SM082
82.791
SM083
66.846
SM084
90.377
SM085
93.533
SM087
X
SM088
76.276
+
SM089
89.148
SM091
88.640
SM092
111.512
SM093
84.960
SM094
88.671
SM097
95.766
+
+
SM098
83.985
SM099
89.837
SM103
94.652
SM104
78.434
SM105
X
SM110
97.923
+
SM112
98.163
SM116
X
SM120
82.223
SM124
74.239
SM125
99.338
SM126
X
+
+
SM127
92.884
SM129
102.170
SM130
75.796
SM131
72.122
SM132
X
SM133
78.205
+
SM134
72.410
SM135
X
SM136
69.277
SM137
94.258
SM139
80.377
SM140
83.032
+
+
SM141
93.925
SM142
94.571
SM143
94.105
SM144
87.311
SM145
X
SM146
61.540
+
SM147
72.827
SM149
83.806
SM150
86.658
SM151
81.326
SM152
80.121
SM153
X
+
+
SM154
X
SM155
95.189
SM156
112.248
SM157
85.789
SM158
107.116
SM159
75.457
+
SM160
X
SM161
88.097
SM162
X
SM164
80.016
SM165
X
SM166
102.909
+
+
SM167
72.578
SM168
73.490
SM169
59.753
SM170
X
SM171
77.510
SM172
X
+
SM173
80.194
SM174
85.298
SM176
98.453
SM177
101.402
SM179
X
SM180
82.275
+
+
SM181
112.517
SM182
X
SM183
106.892
SM184
80.431
SM185
69.175
SM186
118.565
+
SM187
77.768
SM188
87.048
SM189
87.716
SM193
70.069
SM194
85.238
SM196
X
+
+
SM197
93.252
SM198
X
SM199
83.500
SM200
78.391
+
+
Copy the following line to paste into the GeneNetwork entry box:
+60.066 76.919 80.007 122.832 85.447 88.062 109.343 85.448 93.848 88.088 74.384 X 79.413 X 63.176 67.292 95.236 100.175 95.854 85.318 76.069 69.545 101.730 86.738 104.185 X 99.637 104.924 91.376 97.924 68.766 92.028 78.341 88.592 91.877 69.152 92.461 71.237 84.772 88.102 88.222 85.507 82.430 54.067 103.709 99.459 73.284 112.320 80.569 61.621 91.106 80.536 98.238 105.188 83.539 73.012 65.179 89.942 82.730 81.212 98.461 X 92.924 83.156 X 75.906 82.791 66.846 90.377 93.533 X 76.276 89.148 88.640 111.512 84.960 88.671 95.766 83.985 89.837 94.652 78.434 X 97.923 98.163 X 82.223 74.239 99.338 X 92.884 102.170 75.796 72.122 X 78.205 72.410 X 69.277 94.258 80.377 83.032 93.925 94.571 94.105 87.311 X 61.540 72.827 83.806 86.658 81.326 80.121 X X 95.189 112.248 85.789 107.116 75.457 X 88.097 X 80.016 X 102.909 72.578 73.490 59.753 X 77.510 X 80.194 85.298 98.453 101.402 X 82.275 112.517 X 106.892 80.431 69.175 118.565 77.768 87.048 87.716 70.069 85.238 X 93.252 X 83.500 78.391
+
+
+ Access to some GN resources is restricted and is limited to users with IDs and passwords. If
+you have restricted access data in GN then you should already have an account. Once a user
+account has been set up for you, you will be able to login, logoff, change your password,
+etc. by completing the form to the right.
+ Please contact Robert W. Williams by email if you have problems accessing
+restricted data sets.
+
+The Bay-0 x Shahdara genetic reference population of 420 recombinant inbred lines (RIL) was created by Olivier Loudet and Sylvain Chaillou between 1997 and 2000 at the INRA in Versailles, France. It is one of the largest publically available Arabidopsis RIL sets and more than 10 times larger than most rodent RILs. Arabidopsis is commonly known as mustard weed, and is one of the favored model organisms used by geneticists and developmental biologists. This plant has a genome consisting of five chromsomes and a total of 125 megabases of DNA, equivalent in length to a single human chromosome. However, the genome is nonetheless rich and contains approximately 26,000 genes. Full sequence data are available for this species. (The Col-0 accession was sequenced.)
+
+
Please site the following publication when using the Bay-0 x Shahdara (BXS) data sets:
+
+
+Loudet O, Chaillou S, Camilleri C, Bouchez D, Daniel-Vedele F (2002) Bay-0 x Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theoretical and Applied Genetics 104:1173-1184 (pdf)
+
+
+
The original set of 420 RILs were derived from a cross between Bay-0 (accession N954) and Shahdara (accession N929); two accessions obtained from the NASC European Arabidopsis Stock Centre. Bay-0 and Shahdara were chosen because of their well characterized genetic, geographical, and ecological differences. Lines were propagated by single seed descent through the sixth generation (F6) without selection. One plant per line was then used for genotyping (420 RILs x 38 markers) and selfed to obtain F7 seeds. F8 seed stock generated by bulk multiplication of F7 plants are available for analysis for 411 of these RILs. Data sets in WebQTL include up to 415 BXS accessions and the two parental stock.
+
+
How to obtain these lines: The entire extant set of 411 lines was donated to the NASC and ABRC in 2002 and is available (Stock number N57920 and CS57920) for £450 / US $720 (academic fee).
+
+
A core set of 18 lines are also available from the NASC and and ABRC (stock numbers N57922 and CS57922) for £25 / US $40 (academic fee). This "Core-Pop18" set is not intended for systems genetics, but rather is used to evaluate trait variability and transgression. This set includes the parental accessions.
+
+
Single lines may also be purchased directly from NASC for £2.25 each plus £8.50 per order and from ABRC for US $4 per order (prices current as of April 2005).
+
+
Please contact Olivier Loudet at loudet@versailles.inra.fr if you have further questions on the availability of seed stock and comments or questions on the genotype or phenotype data sets deposited in the GeneNetwork.
+
+
+
Note on nomenclature: The widely accepted names of these accessions have the form: Bay-0 x Shahdara - 1, Bay-0 x Shahdara - 2, Bay-0 x Shahdara - 432, etc. In the GeneNetwork we have shortened this long form to BXS001, BXS002, BXS432.
+
+
For more information on the Bay-0 x Shadara Arabidopsis thaliana cross, the genotypic data, the genetic maps, and the trait data please visit the INRA Versailles QTL Arabidopsis site.
+
+
For more background on the history, generation, and use of RILs as genetic reference populations for systems genetics please see Silver (1995). Additional useful literature links are provided in the References link at the top center of this page.
+
+
+
+
+
+
About this file:
+
The file started, April 12, 2005 by Olivier Loudet and RWW. Last update RWW, April 15, 2005.
A population of 150 doubled haploid lines developed from the Steptoe x Morex cross by the Hordeum bulbosum method. The parents, Steptoe and Morex, were selected for their diversity of agronomic traits, Steptoe is high yielding, broadly adapted six-rowed feed-type barley. Morex is midwestern also six-rowed cultivar that has been for long time considered as the American malting industry standard.
+
Please cite the following publication when using the Steptoe x Morex (SxM) data sets:
+ Kleinhofs et al (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet (1993) 86:705-712
+
How to obtain these lines:
+ Seeds of the parents and DHLs are available from:
+ Patrick M. Hayes
+ Department of Crop and Soil Science
+ 109 Crop Science Building
+ Oregon State University
+ Corvallis, OR 97331-3002
+
+
+
+Q21861 x SM89010 (QSM): PLEXdb BarleyBase Experiment BB64: Genetic regulation of gene expression of barley in response to stem rust.
+
+
A population of 75 doubled haploid lines developed from a cross of Q21861 and SM89010 Hordeum bulbosum accessions used to study resistance to Pgt isolate TTKS stem rust. Data on this cross from Roger Wise and colleagues (rpwise@iastate.edu, moscou@iastate.edu). For more details please link to PLEXdb at http://www.plexdb.org/modules/PD_browse/popup_experiment_desc.php?experiment_id=1149#
+
+
About this file:
+
+
The file started, July 13, 2006 by RWW. Last update AD, Jan 15, 2010.
BLAT Specificity, Scores, and the Verify Location Button
+
+
+
+
BLAT Specificity provides a simple estimate of the quality of the alignment (specificity) of a group of probes on an array to a specific gene target. Values typically ranges from about 0.5 to 10, and higher values are better. Values less than 2 indicate that a probe sequence is not highly specific to one location in the genome. These probes may still be prefectly usable. Remember, you are interested in alignment to coding sequence (mRNA), but the BLAT function actually tests the entire genome, including regions that are almost never expressed.
+
+
Specificity is computed as a simple ratio between the top (or correct) BLAT score to the second best (or incorrect) alignment. When the second BLAT score is low or null (no second-best alignment), then we declare a specificity value of 10 (great specificity). When the correct alignment is second best (this is not rare), then we declare the BLAT specificity to be 0.5. Values of 0.5 to 1.0 typically mean that probes have several possible matches across the whole genome.
+
+
BLAT Score provide an estimate of the number of nucleotides that align well to one region of the genome. The maximum number can equal the length of the probe or probe set. For Affymetrix probe sets this number will usually be between 60 and 260. For Illumina and Agilent probes this number will typically be between 40 and 60.
+
+
You can replicate the BLAT analysis by clicking on the Verify function button (one of the large square icons on Trait Data and Analysis page). This button triggers a new request to align the probe sequences to the most recent assembly of the genome using the UCSC Genome Browser Blat function. For example if you click on this button while viewing Affymetrix probe set 1421393_at, the following long and tedious command will be sent by GeneNetwork to the UCSC Genome Browser (this string of text is called a "get" command):
+
+
A BLAT Search Results window will appear that lists the best matches of this sequence in the genome; in this case on mouse Chr 7 at 45.700822 Mb.
+
+
+
+
+
+
Legend: The first Verify output page from the Genome Browser lists the best genomic matches to the sequence of Affymetrix probe set 1421393_at. The best match has a score of 201 out of 207 nucleotides. One poor alignment (score of 25) is also given for the whole probe set to Chr 8 (an intron in Nfix. The individual probes are also listed and they have perfect scores, given their short length (25 of 25).
+
+
+
To the far left of the BLAT Search Results page you will see links that are labeled browser. Click on the top line and you will see a small segment of the genome that matches the sequence on the array. Click on the 10xzoom out button in order to see a bit more of the chromosome and the genes in the local region.
+
+
+
+
+
+
+
Legend: A typical Verify output page from the Genome Browser shows the alignment of Affymetrix probe set 1421393_at and its constituent set of eleven short (25 nucleotide) probes. The probe set is aligning to the negative strand (reading from right to left). The corresponding part of the Grin2d gene is shown in blue toward the bottom (the last exon and 3' untranslated region).
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/web/bug0.html b/web/bug0.html
new file mode 100755
index 00000000..bb57a4aa
--- /dev/null
+++ b/web/bug0.html
@@ -0,0 +1,1742 @@
+
Bug Report Form
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 493, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ' Table1.Name=Table3.Name , Table2.Name=Table3.Name GROUP BY Table1.Name) as Com' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 493, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ' Table1.Name=Table3.Name , Table2.Name=Table3.Name GROUP BY Table1.Name) as Com' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 494, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ' Table1.Name=Table3.Name , Table2.Name=Table3.Name GROUP BY Table1.Name) as Com' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 539
+ i += 1
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 577
+ i += 1
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 577
+ i += 1
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 554
+ SearchText.append(HT.Italic('match the term '), Id='green'))
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 555
+ ttext.append(HT.Italic('match the term '), Id='green'))
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in __init__
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+AttributeError: 'NoneType' object has no attribute 'prefix'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in __init__
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+AttributeError: 'NoneType' object has no attribute 'prefix'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in __init__
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+AttributeError: 'NoneType' object has no attribute 'prefix'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in __init__
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+AttributeError: 'NoneType' object has no attribute 'prefix'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in __init__
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+AttributeError: 'NoneType' object has no attribute 'prefix'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in __init__
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 86, in
+ self.dbPrefix = map(lambda X: X.prefix, self.dbInfos)
+AttributeError: 'NoneType' object has no attribute 'prefix'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 493, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'GROUP BY Table1.Name) as CombineTable WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetI' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 493, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'GROUP BY Table1.Name) as CombineTable WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetI' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 493, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'GROUP BY Table1.Name) as CombineTable WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetI' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 493, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'GROUP BY Table1.Name) as CombineTable WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetI' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 494, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'GROUP BY Table1.Name) as CombineTable WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetI' at line 1")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 226, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, variance = _vars, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/cgi-bin/Yanhua/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/Yanhua/dataPage.py", line 930, in __init__
+ fd.readGenotype()
+ File "/node_apps/www/cgi-bin/Yanhua/DataForm.py", line 132, in readGenotype
+ self.genotype_1.read(os.path.join(CONFIG_genodir, self.RISet + '.geno'))
+SystemError: The given file doesn't exist
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/dataPage.py", line 882, in __init__
+ fd.readGenotype()
+ File "/home/hqli/public_html/cgi-bin/beta/DataForm.py", line 131, in readGenotype
+ self.genotype_1.read(os.path.join(CONFIG_genodir, self.RISet + '.geno'))
+SystemError: The given file doesn't exist
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/cgi-bin/Yanhua/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/Yanhua/dataPage.py", line 930, in __init__
+ fd.readGenotype()
+ File "/node_apps/www/cgi-bin/Yanhua/DataForm.py", line 132, in readGenotype
+ self.genotype_1.read(os.path.join(CONFIG_genodir, self.RISet + '.geno'))
+SystemError: The given file doesn't exist
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/cgi-bin/Yanhua/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/Yanhua/dataPage.py", line 930, in __init__
+ fd.readGenotype()
+ File "/node_apps/www/cgi-bin/Yanhua/DataForm.py", line 132, in readGenotype
+ self.genotype_1.read(os.path.join(CONFIG_genodir, self.RISet + '.geno'))
+SystemError: The given file doesn't exist
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 33, in ?
+ fd = FormData(formdata)
+ File "/node_apps/www/cgi-bin/DataForm.py", line 99, in __init__
+ f1, self.mpolar, self.ppolar = ParInfo[self.RISet]
+KeyError: 'BDF2-2005'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 33, in ?
+ fd = FormData(formdata)
+ File "/node_apps/www/cgi-bin/DataForm.py", line 99, in __init__
+ f1, self.mpolar, self.ppolar = ParInfo[self.RISet]
+KeyError: 'BDF2-2005'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/dataPage.py", line 882, in __init__
+ fd.readGenotype()
+ File "/home/hqli/public_html/cgi-bin/beta/DataForm.py", line 131, in readGenotype
+ self.genotype_1.read(os.path.join(CONFIG_genodir, self.RISet + '.geno'))
+SystemError: The given file doesn't exist
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 495
+ print item,
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2815, in __init__
+ LRSResult = _genotype.regression(_strains, _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 136, in ?
+ page = editHtmlPage(fd)
+ File "/node_apps/www/cgi-bin/upddataPage.py", line 1060, in __init__
+ fp = open(fileName, 'wb')
+IOError: [Errno 2] No such file or directory: '/node_apps/www/html/webqtl//webqtl/main.py'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2815, in __init__
+ LRSResult = _genotype.regression(_strains, _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/beta/intervalPage.py", line 2815, in __init__
+ LRSResult = _genotype.regression(_strains, _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2815, in __init__
+ LRSResult = _genotype.regression(_strains, _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+NameError: name 'MultipleIntMappingPage' is not defined
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 435, in __init__
+ self.cursor.execute(item)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1139, "Got error 'parentheses not balanced' from regexp")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 73, in ?
+ page = ResultsPage(fd)
+ File "/node_apps/www/cgi-bin/resultPage.py", line 153, in __init__
+ resultstable = self.GenReport(fd, _genotype, _strains, _vals, _vars)
+ File "/node_apps/www/cgi-bin/resultPage.py", line 163, in GenReport
+ qtlresults = _genotype.regression(strains = _strains, trait = _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 73, in ?
+ page = ResultsPage(fd)
+ File "/node_apps/www/cgi-bin/resultPage.py", line 153, in __init__
+ resultstable = self.GenReport(fd, _genotype, _strains, _vals, _vars)
+ File "/node_apps/www/cgi-bin/resultPage.py", line 163, in GenReport
+ qtlresults = _genotype.regression(strains = _strains, trait = _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 140, in ?
+ page2 = CorrelationPage(fd)
+ File "/node_apps/www/cgi-bin/correlationPage.py", line 116, in __init__
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1146, "Table 'db_webqtl.ProbeSetXRef' doesn't exist")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 140, in ?
+ page2 = CorrelationPage(fd)
+ File "/node_apps/www/cgi-bin/correlationPage.py", line 116, in __init__
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1146, "Table 'db_webqtl.ProbeSetXRef' doesn't exist")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 124, in ?
+ page=CorrelationPage(fd)
+ File "/node_apps/www/cgi-bin/correlationPage.py", line 116, in __init__
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1146, "Table 'db_webqtl.ProbeSetXRef' doesn't exist")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 124, in ?
+ page=CorrelationPage(fd)
+ File "/node_apps/www/cgi-bin/correlationPage.py", line 116, in __init__
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1017, "Can't find file: './db_webqtl/ProbeSetXRef.frm' (errno: 13)")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2815, in __init__
+ LRSResult = _genotype.regression(_strains, _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 146, in ?
+ page3 = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2815, in __init__
+ LRSResult = _genotype.regression(_strains, _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2815, in __init__
+ LRSResult = _genotype.regression(_strains, _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16
+ thekeys = fd.keys
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16
+ for key in fd.keys:
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16
+ for akey in fd.formdata.keys:
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 17
+ print fd.formdata.keys
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 17
+ print 'fd.formdata.keys'
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 160, in ?
+ from searchPage import *
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16
+ self.database = fd.formdata.getvalue('database', '')
+ ^
+ SyntaxError: invalid syntax
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16, in __init__
+ print fd.formdata.keys.length
+AttributeError: 'function' object has no attribute 'length'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16, in __init__
+ print length(fd.formdata.keys)
+NameError: global name 'length' is not defined
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16, in __init__
+ print len(fd.formdata.keys)
+TypeError: len() of unsized object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16, in __init__
+ print len(fd.formdata.list())
+TypeError: 'list' object is not callable
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16, in __init__
+ print len(fd.formdata.getlist())
+TypeError: getlist() takes exactly 2 arguments (1 given)
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 16, in __init__
+ print fd.formdata.getkeys()
+ File "/usr/src/build/475206-i386/install/usr/lib/python2.3/cgi.py", line 533, in __getattr__
+ raise AttributeError, name
+AttributeError: getkeys
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 18, in __init__
+ print fd.formdata.getValue('database')
+ File "/usr/src/build/475206-i386/install/usr/lib/python2.3/cgi.py", line 533, in __getattr__
+ raise AttributeError, name
+AttributeError: getValue
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 945, in __init__
+ nstrains = [[None]] * len(traitdata)
+TypeError: len() of unsized object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 170, in ?
+ page = ShowDatabasePage(fd)
+ File "/node_apps/www/cgi-bin/dataPage.py", line 872, in __init__
+ fd.RISet = self.cursor.fetchall()[0][0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 77, in __init__
+ self.databaseCrosses, self.databaseCrossIds= self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 566, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 303, in ?
+ page = cmdCorrelation(fd)
+ File "/node_apps/www/cgi-bin/TextUI.py", line 433, in __init__
+ self.readDB()
+ File "/node_apps/www/cgi-bin/TextUI.py", line 555, in readDB
+ self.cursor.execute(query)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+OperationalError: (1054, "Unknown column 'LocusID' in 'field list'")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 112, in ?
+ page = ClusterTreePage(fd)
+ File "/node_apps/www/cgi-bin/correlationPage.py", line 1148, in __init__
+ qtlresult = fd.genotype.regression(strains = _strains, trait = _vals)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 228, in __init__
+ LRSArray = _genotype.permutation(strains = _strains, trait = _vals, nperm=fd.nperm)
+IndexError: the length of the strain list and the value list are different,
+or they are less than 8
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 358, in __init__
+ gifmap = self.plotIntMapping(intCanvas, _LRSResult, _bootResult, fd, offset = (75, 120, 80, 10))
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2374, in plotIntMapping
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+TypeError: unsubscriptable object
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 136, in ?
+ page = editHtmlPage(fd)
+ File "/node_apps/www/cgi-bin/upddataPage.py", line 1060, in __init__
+ fp = open(fileName, 'wb')
+IOError: [Errno 13] Permission denied: '/node_apps/www/html/webqtl//dbdoc/HC_M2_1005_P.html'
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 56, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 56, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 56, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 56, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 56, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 56, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 57, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/home/hqli/public_html/cgi-bin/beta/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/home/hqli/public_html/cgi-bin/beta/searchPage.py", line 57, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "/node_apps/www/webqtl/main.py", line 162, in ?
+ page = SearchResultPage(fd)
+ File "/node_apps/www/cgi-bin/searchPage.py", line 56, in __init__
+ indId, indName, indFullName, indConfid = self.cursor.fetchall()[0]
+IndexError: tuple index out of range
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 519, in __init__
+ mainAreas = self.plotIntMappingALEX_TEST(intCanvas, _LRSResult, _bootResult, fd, geneTable=geneTableMain, offset= (self.WIDTH_LEFT_OFFSET_DEFAULT, self.WIDTH_RIGHT_OFFSET_DEFAULT, self.HEIGHT_TOP_OFFSET_DEFAULT, self.HEIGHT_BOTTOM_OFFSET_DEFAULT), zoom = 1)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 1786, in plotIntMappingALEX_TEST
+ geneCol.loadGenesOnChr(chrName, self.cursor, self.diffCol, self.startMb, self.endMb, fd.identification)
+ File "/node_apps/www/cgi-bin/GeneCollection.py", line 88, in loadGenesOnChr
+ cursor.execute("SELECT count(id) FROM SNP_perlegen where mb > %f and mb < %f and chr = '%s' and %s=1" % (gene[4]-0.002, gene[5]+0.002, tempChr, diffCol))
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1146, "Table 'db_webqtl.SNP_perlegen' doesn't exist")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 519, in __init__
+ mainAreas = self.plotIntMappingALEX_TEST(intCanvas, _LRSResult, _bootResult, fd, geneTable=geneTableMain, offset= (self.WIDTH_LEFT_OFFSET_DEFAULT, self.WIDTH_RIGHT_OFFSET_DEFAULT, self.HEIGHT_TOP_OFFSET_DEFAULT, self.HEIGHT_BOTTOM_OFFSET_DEFAULT), zoom = 1)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 1786, in plotIntMappingALEX_TEST
+ geneCol.loadGenesOnChr(chrName, self.cursor, self.diffCol, self.startMb, self.endMb, fd.identification)
+ File "/node_apps/www/cgi-bin/GeneCollection.py", line 88, in loadGenesOnChr
+ cursor.execute("SELECT count(id) FROM SNP_perlegen where mb > %f and mb < %f and chr = '%s' and %s=1" % (gene[4]-0.002, gene[5]+0.002, tempChr, diffCol))
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1146, "Table 'db_webqtl.SNP_perlegen' doesn't exist")
+
+
+
+
+
Bug Report
Traceback (most recent call last):
+ File "./cmdLine.py", line 120, in ?
+ page = MultipleIntMappingPage(fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 2733, in __init__
+ IntMappingPage.__init__(self,fd)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 519, in __init__
+ mainAreas = self.plotIntMappingALEX_TEST(intCanvas, _LRSResult, _bootResult, fd, geneTable=geneTableMain, offset= (self.WIDTH_LEFT_OFFSET_DEFAULT, self.WIDTH_RIGHT_OFFSET_DEFAULT, self.HEIGHT_TOP_OFFSET_DEFAULT, self.HEIGHT_BOTTOM_OFFSET_DEFAULT), zoom = 1)
+ File "/node_apps/www/cgi-bin/intervalPage.py", line 1786, in plotIntMappingALEX_TEST
+ geneCol.loadGenesOnChr(chrName, self.cursor, self.diffCol, self.startMb, self.endMb, fd.identification)
+ File "/node_apps/www/cgi-bin/GeneCollection.py", line 88, in loadGenesOnChr
+ cursor.execute("SELECT count(id) FROM SNP_perlegen where mb > %f and mb < %f and chr = '%s' and %s=1" % (gene[4]-0.002, gene[5]+0.002, tempChr, diffCol))
+ File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 137, in execute
+ self.errorhandler(self, exc, value)
+ File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler
+ raise errorclass, errorvalue
+ProgrammingError: (1146, "Table 'db_webqtl.SNP_perlegen' doesn't exist")
+
+
+Software license: GeneNetwork source code is available under the GNU Affero General Public License, version 3 (AGPLv3). Source is written in Python, C, and JavaScript. Please contact RW Williams for a status report and access to code. A SourceForge repository is planned for Fall 2010.
+
+
+The QTL Reaper module of GeneNetwork that is used by several mapping modules of GeneNetwork is available under the GNU General Public License at SourceForge.
+
+
+Data sets that have been incorporated in the GeneNetwork belong to individuals, groups, and companies listed in the Status and Contacts page. Many data sets are still being generated and analyzed, and the data contributors have often agreed to remove protection and let other investigators view, share, and analyze data. We request that those of you analyzing these data and preparing publications do your best of acknowledge the original data sources. Please contact Robert W. Williams if you have questions regarding the status of data and what group to acknowledge.
+
+
If your work relies heavily on the GeneNetwork please consider acknowledging the grants that provide substantial support for this project (see bottom of all web pages). Please review the annotated References for relevant citations. For further details on use and citation of data in papers please read the section below on Academic, educational, and not-for-profit institutional use.
+
+
+
+Commercial use of open GeneNetwork data sets is allowed. If GeneNetwork is useful to you and your company then we would like to enlist you as a corporate sponsor. Any use GeneNetworkdoes not include a license to any patent rights that any of the data providers may have that are independent of the database itself.
+
+
+
+
+The Standard Disclaimers of Warranties. The use of GeneNetwork and data sets is provided free of charge. GeneNetwork is an experimental resource and all users should know that GeneNetwork contains coding and data errors--most of which are still unknown to data providers and programmers. As a result we do not and cannot provide any warranty regarding data or results generated using GeneNetwork. Please contact Robert W. Williams (email link at the bottom of each web page) if you suspect that data or results are erroneous.
+
+
The University of Tennessee (UT), its trustees, directors, officers, employees, and affiliates make no representation and extend no warranties of any kind, either express or implied, including warranties of correctness, accuracy, fitness for a particular purpose, merchantability, validity of patent rights claims (issued or pending), the absence of latent or other defects, whether or not discoverable. In no event shall UT or its trustees, directors, officers, employees, or affiliates be liable for incidental or consequential damages of any kind, including economic damage or injury to property and lost profits, regardless of whether UT, its trustees, directors, officers, employees, and affiliates shall be advised, shall have other reason to know, or in fact shall know of the possibility of the foregoing.
+
+
+
+
+Large data sets. Data sets that have not been used in full publications will generally not be available for bulk downloading, redistribution, or analysis by other groups or in other databases without prior written agreement of those who generated the data. It is often possible to obtain access to entire unpublished data sets or large subsets of data on a collaborative basis. Please contact the data owner.
+
+
This restriction on bulk analysis is removed after component databases have led to full publications. Access to full data sets is available at our Data Sharing Zone.
+
+
+
+
+Academic, educational, not-for-profit institutional use, or for-profit users.
+
+All public data in the GeneNetwork are currently available for analyses with the expectation that the particular data sources and providers will be acknowledged and cited appropriately in works or publications. Some data sets are still being generated, revised, expanded, or error-checked. We therefore recommend contacting groups who are generating these data. They will be able to help you analyze, interpret, and confirm results.
+
+
+
+Acknowledgement is appropriate when (1) data taken from GeneNetwork play a minor or supporting role in a study or work, and (2) when you do not need assistance with the interpretation or analysis of the data, and (3) when data are used for research or educational purposes only. Data contributors usually annotate data sets (see the INFO pages), but some of these experiments are complex, and the annotation is often not complete. We recommend contacting the individuals and groups who generated data.
+
+
+
+Co-authorship is appropriate to consider when data taken from GeneNetwork play a pivotal role in a study or when the interpretation or findings require insight into experimental details and statistical design (the metadata).
+
+
+
+
+Disclaimer. The data providers make no guarantees or warranties as to the accuracy or completeness of or results to be obtained from accessing and using information from The GeneNetwork. We will not be liable to any user or anyone else for any inaccuracy, error or omission, regardless of cause, in the data contained in The GeneNetwork databases or any resulting damages. In addition, the data providers do not warrant that the databases will meet your requirements, be uninterrupted, or error-free. Data providers expressly exclude and disclaim all expressed and implied warranties of merchantability and fitness for a particular purpose. Data providers shall not be responsible for any damage or loss of any kind arising out of or related to your use of the databases, including without limitation data loss or corruption, regardless of whether such liability is based in tort, contract, or otherwise.
+
+
+
+
Information about this text file:
+
+
+
This text file originally generated by RWW, March 2004. Updated by RWW, Nov 12, 2004; Dec 4, 2004; April 27, 2005; Sept 1, 2005; Sept 13, 2010.
+
+
+
+ THE INFORMATICS CENTER FOR NEUROGENETICS MAKES NO REPRESENTATION ABOUT THE
+ SUITABILITY OR ACCURACY OF THIS SOFTWARE OR DATA FOR ANY PURPOSE, AND MAKES NO
+ WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE OR THAT THE USE OF THIS SOFTWARE OR DATA WILL NOT INFRINGE ANY
+ THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS, OR OTHER RIGHTS. THE SOFTWARE AND
+ DATA ARE PROVIDED "AS IS".
+
+
+ This software and data are provided to enhance knowledge and encourage progress in the
+ scientific community and are to be used only for research and educational purposes. Any
+ reproduction or use for commercial purpose is prohibited without the prior express written
+ permission of The Informatics Center for Neurogenetics.
+
+
Literature correlations are calculated using the Semantic Gene Organizer (SGO). The SGO software uses a concept-based vector space model called latent semantic indexing (LSI) to automatically extract gene-gene relations from titles and abstracts in MEDLINE citations (Homayouni et al. 2005).
+
+
These LSI literature correlations are all positive and range from 0 to 1. They were computed in mid 2005 using the complete PubMed collection. They were recomputed in 2007 by Dr. Ramin Homayouni and colleagues and entered into GeneNetwork by Nick Furlotte.
+
+
Vector space modeling is a classical information retrieval technique used to identify conceptually related documents, whereby the semantic structure of a document is represented as a vector in word space and the degree of similarity between documents is calculated by the angle between document vectors. LSI improves retrieval by using a singular value decomposition (or principal component analysis) to create a subspace of concepts in which text documents are represented as vectors.
+
+
Each gene is represented as a vector in word or concept space. The cosine of the angle between the query gene vector and all other gene vectors is used to rank related genes. The distribution of cosine values ranges between 1 and -1, where a value of 1 denotes the highest similarity.
+
+
An important advantage of LSI over other vector-based retrieval methods is that relations can be derived even if a direct link between genes has not been established in the literature. The fewer factors that are used for query matching, the more conceptual the relations, and vice versa. Therefore, genes may be conceptually related even if they have not been studied together directly. This utility of LSI makes it ideal for investigating the functional significance of gene associations identified in discovery oriented genomic studies.
+
+
SGO literature correlation values may be used to rapidly identify known relations between co-regulated genes and the latent relations between co-regulated genes based on current literature.
+
+
+
Methods
+
+
Gene abstract documents are first compiled using titles and abstracts in MEDLINE citations cross-referenced for each mouse gene and its human and rat homologs. These gene documents were assembled and parsed into a dictionary of terms (tokens) and weighted frequencies that are required for the term-by-gene document (sparse) matrix. In effect, each gene document is viewed as a bag of words upon which operations can be performed. There are a number of different word weighting schemes that can be used in vector space modeling (Baeza-Yates and Ribeiro-Neto, 1999). The aim of any scheme is to measure similarity within a document while at the same time measuring the dissimilarity of a gene document from the other gene documents. In SGO, we use a log entropy weighting scheme to decrease the weight of high frequency words, while giving distinguishing words higher weights (Berry and Browne, 1999).
+
+
Term and document vectors for the LSI model deployed by SGO were generated by truncating the singular value decompisition (SVD) of the term-by-gene document matrix to s factors (i.e., only s columns of the orthogonal matrices U and V are used). LSI therefore produces a rank-reduced space in which to compare two gene documents at different conceptual levels. In practice, the maximum number of factors is limited by the number of documents in the collection. Fewer factors may be used for broad (more conceptual) comparisons, whereas a larger number of factors may be used for specific (more literal) comparisons. Other studies have demonstrated that for large documents collections the optimal number of factors is approximately 300 (Landauer et al., 2004).
+
+
The tissue correlation is an estimate of the similarity of expression of two genes or transcripts across different cells, tissues, or organs. Tissue correlations were generated by analyzing gene expression in multiple tissues taken from single animals (C57BL/6J, DBA/2J mice, and BN rats). Both Pearson product-moment correlations and Spearman rank order correlations have been computed for all pair of genes using data from a set of tissue samples. Both correlation types -- r and rho -- as well as their associated p value are displayed in Trait Correlation pages to the far right. While we used mouse tissues to compute the tissue correlations, we display these values even in tables generated for rat and human transcripts and gene.
+
+
This tissue correlation analysis was carried out by Drs. Xusheng Wang, Lu Lu, and Robert W. Williams at the University of Tennessee Health Science Center in collaboration with Illumina Inc. (Jan and Feb 2008) using the MouseWG-6 v2.0 array. The GN interface was created by Xiaodong Zhou. We generated data from approximately 60 samples. The correlations in GeneNetwork were computed for a subset of 25 tissues or tissue pools that have moderately independent expression patterns. We merging many CNS samples into a single pooled value. We also merged data for ileum, jejunum, and duodenum.
+
+
In many cases, the expression of a single gene is estimated by multiple probes or probe sets, multiple exons, or alternative transcripts. In the case of the Illumina array that we used, there are typically two to three probes per gene and all may be equally valid estimates of different aspects of the expression of a gene. To provide an approximate first-order summary of joint expression of genes across tissues we simply selected that probe associated with the single highest estimate of expression averaged across multiple tissues.
+[Dec 2008, RWW].
+
+
+
+
+
+
Conventional Pearson product-moment correlations (r) or Spearman rank order correlations (rho) were computed across approximately 25 different organs and tissue types. The rank order correlations will be less dependent on the distribution of expression estimates or the particular set of 25 tissue types.
+
+
The Tissue P (r) is the probability associated with the Pearson product-moment correlation. The Tissue P (rho) is the corresponding probability associated with the Spearman rank order statistic. Both P values are currently computed for an n of 25 organs and tissue types. The rank order correlation will be more conservative. This p value may be appropriate if the bivariate distribution of points across the plots is normally distributed in both x and y axes.
+
+
+
+
Pearson' s Sample Correlation, r, is computed using trait values measured across a population of genetically diverse cases (individuals or strains). This is the Pearson's r value computed across cases or samples. The correlation is generated by a combination of shared genetic, environmental, and experimental factors. In other words, this is a correlation of phenotypes across a population. It is only a good estimate of a genetic correlation when developmental, environmental, technical, and error variance in the sample is low. In the case of sets of recombinant inbred strains it is possible to reduce non-genetic sources of variance by pooling samples and by resampling genetically identical individuals.
+
+
+
p Value of Sample Correlation (Pearson's r): The p value associated with the Pearson product-moment correlation type described above. The p value takes into account differences in the sample size. Correlations and traits are usually ranked with the smallest p value (most significant) on the top.
+
+
+
Spearman's Sample Correlation, rho, is computed using trait values measured across a population of genetically diverse cases (individuals or strains). This is the Spearman rank order correlation (called rho rather than r) that has been computed across the samples. This correlation is not unduly affected by outliers, and should also generally be used when sample size is small (less than 20). Correlation is generated by a combination of genetic, environmental, and experimental factors. It is only a good estimate of a genetic correlation when developmental, environmental, technical, and error variance in the sample is low. In the case of sets of recombinant inbred strains it is possible to reduce non-genetic sources of variance by pooling samples and by resampling genetically identical individuals.
+
+
+
p Value of Sample Correlation (Spearman's rho): The p value associated with the Spearman rand order correlation type described above. The p value takes into account differences in the sample size. Correlations and traits are usually ranked with the smallest p value (most significant) on the top.
+
+
+
+
+
+
+
+
+
+The AKXD recombinant inbred (RI) strains are derived from AKR/J (AK) and DBA/2J (D). All of these strains were made by Benjamin A. Taylor.
+
+
All of the AKXD data in WebQTL is from an experiment by Kent Hunter and colleagues. WebQTL does not yet include a Phenotypes database for this strain set.
+The AXB and BXA set of recombinant inbred (RI) strains were derived from a reciprocal cross between A/J (A) and C57BL/6J (B). Both parental strains have been sequenced, making this a particularly powerful set of RI strains for functional and genetic analyses. Data acquired using AXB and BXA subsets should be combined; the only difference being the polarity of intercross matings that generated (A x B)F1s and (B x A)F1s. AXB and BXA strains were all produced by Muriel Nesbitt at UCSD in the mid and late 1970s and first used in the early 1980s (Skamene et al., 1984; Peleg and Nesbitt, 1984; Marshal and Paigen, 1993). The set was imported into The Jackson Laboratory by Beverly Paigen (Pgn) in the early 1990s. As of 2004, approximately 25 viable and fully independent AXB/BXA strains are available.
+
+
Approximately 100 traits are currently included in the AXBXA Phenotypes database (Nov 2004).
+
+
+
Several nominally independent strains in the AXB and BXA sets are very closely related. These duplicates should not be used without special statistical precaution. The most obvious option is to combine and average data from these strains except when their phenotypes differ significantly (Taylor 1996; Williams et al., 2001).
+
+
+ AXB13=AXB14: 92% identity
+ AXB18=AXB19=AXB20: 97 to 99% identity
+ BXA8=BXA17: 99.8% identity
+
+The BXD set of recombinant inbred (RI) strains were derived by crossing C57BL/6J (B) and DBA/2J (D) and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). These new strains have roughly twice the number of recombinations of conventional F2-derived RI straons. The new BXD strains are available now from Lu Lu and colleagues.
+
+
The mitochondrial DNA of all BXD strains were typed by Jing Gu and Shuhua Qi (Nov 2004) using DNAs obtained from the Jackson Laboratory (BXD1 through 42) or from the UTHSC colony. This typing relied on a SNP marker identified by Jan Jiao in Weikuan Gu's laboratory at basepair position 9461 in the reference C57BL/6J mitochondrial sequence. Most strains have inherited mitochondria from C57BL/6J. However, the following strains have mitochondria with a DBA/2J allele at the UT-M-9461 SNP: BXD32, 61, 74, 76, 82, 89, 90, 91, 95, and BXD99. The only surprise in this list is that BXD32/TyJ has a DBA/2J mitochondrial genotype.
+
+
Approximately 680 traits are currently included in the BXD Phenotypes database (Nov 2004).
+The BXH set were made by crossing female C57BL/6J (B) with male C3H/HeJ (H) mice. Benjamin Taylor created the initial 12 BXH recombinant inbred strains at The Jackson Laboratory in 1969. A second set of eight BXH strains were initiated by Linda Siracusa at the Kimmel Cancer Center in 1995. She selected for tyrosinase-negative albinos and her strains should not be used to map on Chr 7. Four of these new BXH strains are now also available from The Jackson Laboratory. The following are the old and new symbols for the four recent additions:
+
+
+
BXHA1/Sr = BXH20/Kcc
+
BXHA2/Sr = BXH21/Kcc
+
BXHB2/Sr = BXH22/Kcc
+
BXHE1/Sr = B6cC3-1/Kcc (backcrossed to B6 and a recombinant congenic)
+
+
+
Approximately 135 traits are currently included in the BXH Phenotype database (Nov 2004).
+The CXB set is the first, oldest, and smallest group of mouse recombinant inbred strains. The materal strain is BALB/cBy and the paternal strain is C57BL/6By. They have been used extensively by immunologists and neurogeneticists. A total of 13 of these strains are now available.
+
+
Over 450 traits are now included in the CXB Phenotype database (Nov 2004).
+The parental strains of the LXS recombinant inbred (RI) set are Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) strains. These parental strains have been phenotyped intensively by behavioral geneticists and neuropharmacologists for a decade. The LXS RI set has an intriguing history and trace back to an 8-way cross initiated in the 1950s by Gerald McClearn, the dean of mouse behavior genetics.
+
+
The LXS panel has recently been genotyped at 330 microsatellite markers, and this panel can already be used to map Mendelian and quantitative trait loci.
+
+
This is a new RI panel and only a small number of traits are currently included in the LXS Phenotype database (Nov 2004).
+
+
+
For information on the availability of the LXS strains please contact Beth Bennett.
+
+Fifty-six Filial generation 2 (F2) mice were generated by crossing C57BL/6J (B6) and DBA/2J (D2) stock from the Jackson Laboratory. The F1s were mated reciprocally to create B6D2F2 and D2B6F2 progeny. At present , WebQTL includes one large microarray data set (Affymetrix M430) for the entire brain of these F2 progeny.
+
+
+For further information, please contact John Belknap, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland VA Medical Center, Portland, OR 97239.
+This cross consists of a subset of 60 F2 progeny generated by crossing C57BL/6J and BTBR strains. All of these cases are homozygous for the spontaneous obese mutation in the leptin gene (Lep-ob/ob). Metabolic function, liver mRNA expression (Agilent platform), and other physiological and molecular traits related to type 2 diabetes and obesity were quantified. Liver gene expression data were generated by Hong Lan and Alan Attie at The University of Wisconsin-Madison. Please contact Drs. Alan Attie regarding use of this data set in publications or projects.
+
+The Mouse Diversity Panel is simply a composite of common and wild inbred strains and even some isogenic F1 hybrids.
+
+
Over 1000 traits were downloaded from the Mouse Phenome Database at The Jackson Laboratory in June 2006 and implemented in GeneNetwork July 2006.
+
+
When using the MPD please cite this URL:
+http://www.jax.org/phenome. This is the MPD's best known location and is usually preferable to the longer dynamic system URLs that may appear in URL address fields.
+
+
+
Publications:
+
+
Grubb SC, Churchill GA, Bogue MA (2004) A collaborative database of inbred mouse strain characteristics. Bioinformatics. 20:2857-9. PMID: 15130929
+
+
To cite specific phenotyping data in the MPD, a format similar to this may be used. (Please be sure you have read and agree with our user agreement for taking and using MPD data.)
+
+
Investigators. Project Title. MPD accession#. Mouse Phenome Database Web Site, The Jackson Laboratory, Bar Harbor, Maine USA. World Wide Web (URL: http://www.jax.org/phenome, month and year of download ).
+
+
Example:
+
Wahlsten D, Crabbe JC. Comparative study of activity, anxiety, motor learning, and spatial learning in two laboratories. MPD:108. Mouse Phenome Database Web Site, The Jackson Laboratory, Bar Harbor, ME USA. World Wide Web (URL: http://www.jax.org/phenome, July 2004).
+
+
Each phenotyping project in the MPD is assigned an accession number having the format MPD:NNN, where NNN is an integer. Accession numbers are displayed in the projects index and the individual project detail pages.
+
+
+
+
+For a summary of the NIH Guidelines on data sharing see http://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm. This document provides guidelines primarily intended for those who are acquiring data and metadata obtained as part of large scale NIH-funded projects (greater than $500,000 in direct costs in any one year). Contributors to The GeneNework and WebQTL are at the vanguard in terms of data sharing and have made data sets available within days of acquisition, transformation, and error-checking. "Sharing" however is not equivalent to "free distribution." We anticipate reciprocal contributions from you in the form of one or more of the following: acknowledgement of data sources and use of The GeneNetwork and WebQTL, communication with and possible collaboration with our colleagues who have provided data, suggestions for improvements, and best of all, contributions of new data sets. We hope that you will contribute to the annotation, use, and extension of these data sets in ways that are rewarding to all who are involved.
+
+
+
+Wellcome Trust-NIH data sharing recommentations.
+An excellent set of recommendations on Data Sharing from Large-scale Biological Research Projects have been assembled with the help of The Wellcome Trust (January 2003, Ft. Lauderdale meeting). These Data Sharing Policies have been adopted in large part by the Encode project. Like GeneNetwork, Encode is a distributed effort by many investigators to integrate a variety of data into a common knowledgebase. Both documents are worth reading by if you are using the GeneNetwork for publications. They may also be particularly helpful for groups considering submitting data sets to the GeneNetwork.
+
+
+
+
+Please see http://datasharing.net/ for a series of cogent and succinct abstracts on the practice and ethics of data sharing. We particularly recommend reviewing Data Sharing IV.
+
+
+
+
+NIH data sharing conditions.
+
+Data sets generated primary or exclusively using NIH funds covered under the Data Sharing Policy (effective after October 2003) will be made available as open resources to academic and non-profit organizations for their own research purposes in a timely manner. "Timely" means no later than the acceptance date for publication of the main findings derived from the relevant data set. In the case of Affymetrix and other high-throughput genomic screening methods, the data release will include (when available) the original images, probe-level data, probe set data, and report files.
+
+
+
+
Information about this text file:
+
This text file originally generated by RWW, March 2004. Updated by RWW, Nov 12, 2004; Sept 1, 2005.
+
+
+GenomeGraph is designed to help discover genetic sources of variation in trait and transcript expression at a global level. Choose a database and click on the Mapping button. The y-axis marks the physical locations of genes from which transcripts are synthesized. In contrast, the x-axis plots the locations of the highest LRS values associated with each trait or transcript; in essence, the location of the best QTL. The false discovery rate (FDR) can be tuned from 1 (all data shown) to values between 0.1 and 0.01 (only transcripts with significant QTLs shown).
+
+
Note that many data set results are still being computed. You may encounter an "in progress" message.
+
+
For a more complete explanation see Chesler, Lu and colleagues (2005), or the GenomeGraph Help page.
+
Download the entire AKXD genotype file used in GeneNetwork (n = 1352 markers with useful strain distribution pattens from a total of 5448 informative markers). We have modified the orginal Wellcome-CTC genotypes by adding selected microsatellite markers. We have also curate the data and have removed somewhat improbable double-recombinant haplotypes and by imputing genotypes for a few untyped strains using very tightly linked markers. This genotype "smoothing" may remove some genuine recombinations and may result in linkage maps that will be very slightly conservative.
+
+
+
Download the entire AXB/BXA genotype file used in GeneNetwork (n = 2446 unique strain distribution patterns based on a total of 8514 informative markers). We have modified the orginal Wellcome-CTC genotypes by adding selected microsatellite markers. We have also curate the data and have removed somewhat improbable double-recombinant haplotypes and by imputing genotypes for a few untyped strains using very tightly linked markers. This genotype "smoothing" may remove some genuine recombinations and may result in linkage maps that will be very slightly conservative.
+
+
+
+
About the cases used in these studies:
+
+
+The AXB and BXA recombinant inbred strains were derived from a reciprocal cross between A/J (A) and C57BL/6J (B6 or B). Both parental strains have been sequenced, making this a particularly powerful set of RI strains for functional and genetic analyses. Data acquired using AXB and BXA subsets should be combined; the only difference being the polarity of intercross matings that generated (A x B)F1s and (B x A)F1s. AXB and BXA strains were all produced by Muriel Nesbitt at UCSD in the mid and late 1970s and first used in the early 1980s (Skamene et al., 1984; Peleg and Nesbitt, 1984; Marshal and Paigen, 1993). The set was imported into The Jackson Laboratory by Beverly Paigen (Pgn) in the early 1990s. As of 2004, approximately 25 viable and fully independent AXB/BXA strains are available.
+
+
+
+
Several nominally independent strains in the AXB and BXA sets are very closely related. These duplicates should not be used without special statistical precaution. The most obvious option is to combine and average data from these strains except when their phenotypes differ significantly (Taylor 1996; Williams et al., 2001).
+
+
+ AXB13=AXB14: 92.74% identity in an analysis of 8429 markers. AXB14/PgnJ (JAX001684) was renamed AXB13a/PgnJ (see JAXNotes issue number 504, Winter 2006).
+ AXB18=AXB19=AXB20: 97 to 99% identity (AXB18 to AXB19 = 98.16% identity, AXB18 to AXB20 = 95.72% identity, AXB19 to AXB20 = 97.34% identity n an analysis of 8429 markers). AXB18 (JAX001686) was renamed AXB19a; AXB19 (JAX001687) was NOT renamed and is still AXB19, and AXB20 (JAX001688) was renamed AXB19b (see JAXNotes issue number 504, Winter 2006).
+ BXA8=BXA17: 99.79% identity in an analysis of 8429 markers. BXA17 has been discarded as a strain. The orginal BXA17 was lost between 1989 and 1990. (Updated from Williams et al. 2001; see JAXNotes issue number 504, Winter 2006).).
+
+
+
+
+
About the genotypes associated with these strains:
Published phenotypes were obtained through a literature search of all PubMed indexed journals. Whenever possible, exact values of graphically represented data were obtained from the authors. In all other cases graphs were measured using a vernier caliper. Additional published and unpublished phenotypes were submitted directly by investigators. These records have Record ID numbers less than 1.
+
+
+
+
The special AXB/BXA genotype data set that we use in GeneNetwork may be download as a "AXBXA.geno" file and opened with any text editor or even a spreadsheet program. This file is tab-delimited and includes the approximately centimorgan and basepair (megabasepair) location of the marekers, as well as the genotypes. Genotypes for several sets of strains have been combined. To obtain the original uncombined genotypes, please link to http://www.well.ox.ac.uk/mouse/INBREDS/ .
+
The utility of the AXB/BXA phenotype database increases significantly as each new phenotype is incorporated. To submit new data or report errors, please contact Elissa J. Chesler and Robert W. Williams at University of Tennessee Health Science Center
+
+
+
Acknowledgments:
+
+The initial construction of this phenotype database was performed with the help of Ryan McNeive, Nathan Copeland, and Mary-Kathleen Sullivan at University of Tennessee Health Sciences Center with support by a Human Brain Project to RWW. The extension and curation of these RI phenotype files is managed by Elissa J. Chesler.
+
+
+
References:
+
+
+Peleg L, Nesbitt MN (1984) Genetic control of thymus size in inbred mice. J Hered. 75:126-130.
+
+
+Skamene E, James SL, Meltzer MS, Nesbitt MN (1984) Genetic control of macrophage activation for killing of extracellular targets. J Leukoc Biol 35:65-69.
+
+
+Sampson SB, Higgins DC, Elliot RW, Taylor BA, Lueders KK, Koza RA, Paigen B (1998) An edited linkage map for the AXB and BXA recombinant inbred mouse strains. Mamm Genome 9:688-694.
+
+
+Williams RW, Gu J, Qi S, Lu L (2001) The genetic structure of recombinant inbred mice: High-resolution consensus maps for complex trait analysis. Genome Biology 2:RESEARCH0046.
+
+
+
+
Information about this text file:
+
This text file was originally written by EJC, March 2004. Updated by RWW, October 30, 2004, EJC June 6, 2005.
+
+This AXB/BXA Phenotype Database includes published trait data for up to 27 recombinant inbred strains. Data were collected and curated at the University of Tennessee Health Science Center (UTHSC) starting in 2000. New traits are still being added.
+
+
+
+
About the cases used in these studies:
+
+
+The AXB and BXA recombinant inbred strains were derived from a reciprocal cross between A/J (A) and C57BL/6J (B6 or B). Both parental strains have been sequenced, making this a particularly powerful set of RI strains for functional and genetic analyses. Data acquired using AXB and BXA subsets should be combined; the only difference being the polarity of intercross matings that generated (A x B)F1s and (B x A)F1s. AXB and BXA strains were all produced by Muriel Nesbitt at UCSD in the mid and late 1970s and first used in the early 1980s (Skamene et al., 1984; Peleg and Nesbitt, 1984; Marshal and Paigen, 1993). The set was imported into The Jackson Laboratory by Beverly Paigen (Pgn) in the early 1990s. As of 2004, approximately 25 viable and fully independent AXB/BXA strains are available.
+
+
+
Several nominally independent strains in the AXB and BXA sets are very closely related. These duplicates should not be used without special statistical precaution. The most obvious option is to combine and average data from these strains except when their phenotypes differ significantly (Taylor 1996; Williams et al., 2001).
+
+
+ AXB13=AXB14: 92% identity
+ AXB18=AXB19=AXB20: 97 to 99% identity
+ BXA8=BXA17: 99.8% identity
+
+
+
AXB18/PgnJ is now referred to as AXB19a/PgnJ (JAX stock number 001686)
+
AXB20/PgnJ is now referred to as AXB19b/PgnJ (JAX stock number 001688)
+
+
+
+
About the genotypes associated with these strains:
Published phenotypes were obtained through a literature search of all PubMed indexed journals. Whenever possible, exact values of graphically represented data were obtained from the authors. In all other cases graphs were measured using a vernier caliper. Additional published and unpublished phenotypes were submitted directly by investigators. These records have Record ID numbers less than 1.
+
The utility of the AXB/BXA phenotype database increases significantly as each new phenotype is incorporated. To submit new data or report errors, please contact Elissa J. Chesler and Robert W. Williams at University of Tennessee Health Science Center
+
+
+
Acknowledgments:
+
+The initial construction of this phenotype database was performed with the help of Ryan McNeive, Nathan Copeland, and Mary-Kathleen Sullivan at University of Tennessee Health Sciences Center with support by a Human Brain Project to RWW. The extension and curation of these RI phenotype files is managed by Elissa J. Chesler.
+
+
+
References:
+
+
+Peleg L, Nesbitt MN (1984) Genetic control of thymus size in inbred mice. J Hered. 75:126-130.
+
+
+Skamene E, James SL, Meltzer MS, Nesbitt MN (1984) Genetic control of macrophage activation for killing of extracellular targets. J Leukoc Biol 35:65-69.
+
+
+Sampson SB, Higgins DC, Elliot RW, Taylor BA, Lueders KK, Koza RA, Paigen B (1998) An edited linkage map for the AXB and BXA recombinant inbred mouse strains. Mamm Genome 9:688-694.
+
+
+Williams RW, Gu J, Qi S, Lu L (2001) The genetic structure of recombinant inbred mice: High-resolution consensus maps for complex trait analysis. Genome Biology 2:RESEARCH0046.
+
+
+
+
Information about this text file:
+
This text file was originally written by EJC, March 2004. Updated by RWW, October 30, 2004, EJC June 6, 2005.
+
Barley1 Embryo MAS 5.0 SCRI (Dec 06) - integrated probe set value for each gene has been calculated using MAS 5.0 algorithm which uses pixel values from both, PM and MM probes. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
+
+
Summary:
+
+
+
The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip.
+
+
+
About the lines used to generate this set of data:
+
+
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
+
+
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
+1)
+pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
+2)
+'minimapper' subset - MINI;
+3) lines that have expression data removed - ERROR:
+
+
+
+
Order #
+
Line ID
+
Permanent Oregon ID
+
Cross direction
+
CEL file names
+
Mini-mapper set
+
Error check
+
+
+
embryo data-set
+
leaf data-set
+
embryo data-set
+
leaf data-set
+
+
+
1
+
SM001
+
2907001
+
Steptoe/Morex(BxF)
+
AD_SCRI_82.CEL
+
+
+
OK
+
+
+
+
2
+
SM002
+
2907002
+
Steptoe/Morex(BxF)
+
AD_SCRI_1.CEL
+
+
+
OK
+
+
+
+
3
+
SM003
+
2907003
+
Morex/Steptoe(CxF)
+
AD_SCRI_19.CEL
+
+
+
OK
+
+
+
+
4
+
SM004
+
2907004
+
Morex/Steptoe(CxF)
+
AD_SCRI_3.CEL
+
0521-1_SetA1.CEL
+
SMmini
+
OK
+
OK
+
+
+
5
+
SM005
+
2907005
+
Steptoe/Morex(BxH)
+
AD_SCRI_88.CEL
+
+
+
OK
+
+
+
+
6
+
SM006
+
2907006
+
Morex/Steptoe(CxF)
+
AD_SCRI_48.CEL
+
+
+
OK
+
+
+
+
7
+
SM007
+
2907007
+
Steptoe/Morex(BxH)
+
AD_SCRI_35.CEL
+
0521-2_SetA2.CEL
+
SMmini
+
OK
+
OK
+
+
+
8
+
SM009
+
2907009
+
Steptoe/Morex(BxF)
+
AD_SCRI_2.CEL
+
+
+
OK
+
+
+
+
9
+
SM010
+
2907010
+
Morex/Steptoe(IxE)
+
AD_SCRI_42.CEL
+
+
+
OK
+
+
+
+
10
+
SM011
+
2907011
+
Steptoe/Morex(QxG)
+
AD_SCRI_10.CEL
+
+
+
OK
+
+
+
+
11
+
SM012
+
2907012
+
Morex/Steptoe(CxF)
+
AD_SCRI_45.CEL
+
0521-3_SetA3.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
12
+
SM013
+
2907013
+
Morex/Steptoe(IxE)
+
AD_SCRI_78.CEL
+
0521-4_SetA4.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
13
+
SM014
+
2907014
+
Steptoe/Morex(BxH)
+
AD_SCRI_18.CEL
+
+
+
OK
+
+
+
+
14
+
SM015
+
2907015
+
Steptoe/Morex(BxH)
+
AD_SCRI_5.CEL
+
+
+
OK
+
+
+
+
15
+
SM016
+
2907016
+
Steptoe/Morex(BxH)
+
AD_SCRI_21.CEL
+
+
+
OK
+
+
+
+
16
+
SM020
+
2907020
+
Steptoe/Morex(OxJ)
+
AD_SCRI_77.CEL
+
+
+
OK
+
+
+
+
17
+
SM021
+
2907021
+
Morex/Steptoe(IxE)
+
AD_SCRI_30.CEL
+
+
+
OK
+
+
+
+
18
+
SM022
+
2907022
+
Morex/Steptoe(IxE)
+
AD_SCRI_31.CEL
+
0521-5_SetA5.CEL
+
SMmini
+
OK
+
OK
+
+
+
19
+
SM023
+
2907023
+
Steptoe/Morex(BxH)
+
AD_SCRI_32.CEL
+
+
+
OK
+
+
+
+
20
+
SM024
+
2907024
+
Morex/Steptoe(IxE)
+
AD_SCRI_33.CEL
+
0521-6_SetA6.CEL
+
SMmini
+
OK
+
OK
+
+
+
21
+
SM025
+
2907025
+
Morex/Steptoe(CxF)
+
AD_SCRI_34.CEL
+
+
+
OK
+
+
+
+
22
+
SM027
+
2907027
+
Steptoe/Morex(OxJ)
+
AD_SCRI_12.CEL
+
0521-7_SetA7.CEL
+
SMmini
+
OK
+
OK
+
+
+
23
+
SM030
+
2907030
+
Morex/Steptoe(IxE)
+
AD_SCRI_79.CEL
+
+
+
OK
+
+
+
+
24
+
SM031
+
2907031
+
Steptoe/Morex(OxJ)
+
AD_SCRI_16.CEL
+
+
+
OK
+
+
+
+
25
+
SM032
+
2907032
+
Morex/Steptoe(IxE)
+
AD_SCRI_13.CEL
+
+
+
OK
+
+
+
+
26
+
SM035
+
2907035
+
Morex/Steptoe(CxF)
+
AD_SCRI_15.CEL
+
+
+
ERROR
+
+
+
+
27
+
SM039
+
2907039
+
Morex/Steptoe(CxF)
+
AD_SCRI_41.CEL
+
+
+
OK
+
+
+
+
28
+
SM040
+
2907040
+
Steptoe/Morex(BxH)
+
AD_SCRI_83.CEL
+
+
+
OK
+
+
+
+
29
+
SM041
+
2907041
+
Steptoe/Morex(OxJ)
+
AD_SCRI_11_redo.CEL
+
0521-8_SetA8.CEL
+
SMmini
+
OK
+
OK
+
+
+
30
+
SM042
+
2907042
+
Morex/Steptoe(CxF)
+
AD_SCRI_57.CEL
+
+
+
OK
+
+
+
+
31
+
SM043
+
2907043
+
Morex/Steptoe(JxE)
+
AD_SCRI_49.CEL
+
0521-9_SetA9.CEL
+
SMmini
+
OK
+
OK
+
+
+
32
+
SM044
+
2907044
+
Steptoe/Morex(OxJ)
+
AD_SCRI_50.CEL
+
0521-10_SetA10.CEL
+
SMmini
+
OK
+
OK
+
+
+
33
+
SM045
+
2907045
+
Steptoe/Morex(BxH)
+
AD_SCRI_51.CEL
+
+
+
OK
+
+
+
+
34
+
SM046
+
2907046
+
Steptoe/Morex(OxJ)
+
AD_SCRI_52.CEL
+
0521-11_SetA11.CEL
+
SMmini
+
OK
+
OK
+
+
+
35
+
SM048
+
2907048
+
Steptoe/Morex(BxF)
+
AD_SCRI_53.CEL
+
+
+
ERROR
+
+
+
+
36
+
SM050
+
2907050
+
Morex/Steptoe(IxE)
+
AD_SCRI_46.CEL
+
+
+
OK
+
+
+
+
37
+
SM054
+
2907054
+
Morex/Steptoe(CxF)
+
AD_SCRI_60.CEL
+
+
+
OK
+
+
+
+
38
+
SM055
+
2907055
+
Steptoe/Morex(OxJ)
+
AD_SCRI_55.CEL
+
+
+
OK
+
+
+
+
39
+
SM056
+
2907056
+
Steptoe/Morex(BxH)
+
AD_SCRI_23.CEL
+
+
+
OK
+
+
+
+
40
+
SM057
+
2907057
+
Morex/Steptoe(CxF)
+
AD_SCRI_24.CEL
+
+
+
OK
+
+
+
+
41
+
SM058
+
2907058
+
Steptoe/Morex(BxF)
+
AD_SCRI_22.CEL
+
+
+
OK
+
+
+
+
42
+
SM059
+
2907059
+
Steptoe/Morex(BxH)
+
AD_SCRI_27.CEL
+
+
+
OK
+
+
+
+
43
+
SM061
+
2907061
+
Morex/Steptoe(LxF)
+
AD_SCRI_81.CEL
+
0521-12_SetA12.CEL
+
SMmini
+
OK
+
OK
+
+
+
44
+
SM062
+
2907062
+
Morex/Steptoe(CxF)
+
AD_SCRI_44.CEL
+
+
+
OK
+
+
+
+
45
+
SM063
+
2907063
+
Steptoe/Morex(OxJ)
+
AD_SCRI_40.CEL
+
0521-13_SetA13.CEL
+
SMmini
+
OK
+
OK
+
+
+
46
+
SM064
+
2907064
+
Morex/Steptoe(CxF)
+
AD_SCRI_87_redo.CEL
+
+
+
OK
+
+
+
+
47
+
SM065
+
2907065
+
Morex/Steptoe(CxF)
+
AD_SCRI_54.CEL
+
+
+
OK
+
+
+
+
48
+
SM067
+
2907067
+
Steptoe/Morex(OxJ)
+
AD_SCRI_73.CEL
+
+
+
OK
+
+
+
+
49
+
SM068
+
2907068
+
Steptoe/Morex(OxG)
+
AD_SCRI_56.CEL
+
+
+
ERROR
+
+
+
+
50
+
SM069
+
2907069
+
Steptoe/Morex(BxH)
+
AD_SCRI_71.CEL
+
+
+
OK
+
+
+
+
51
+
SM070
+
2907070
+
Steptoe/Morex(BxF)
+
AD_SCRI_64.CEL
+
+
+
OK
+
+
+
+
52
+
SM071
+
2907071
+
Steptoe/Morex(BxH)
+
AD_SCRI_58.CEL
+
+
+
OK
+
+
+
+
53
+
SM072
+
2907072
+
Morex/Steptoe(CxF)
+
AD_SCRI_59.CEL
+
+
+
OK
+
+
+
+
54
+
SM073
+
2907073
+
Steptoe/Morex(BxF)
+
AD_SCRI_74.CEL
+
0521-14_SetA14.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
55
+
SM074
+
2907074
+
Morex/Steptoe(CxF)
+
AD_SCRI_25.CEL
+
0521-15_SetA15.CEL
+
SMmini
+
OK
+
OK
+
+
+
56
+
SM075
+
2907075
+
Steptoe/Morex(QxG)
+
AD_SCRI_120.CEL
+
+
+
OK
+
+
+
+
57
+
SM076
+
2907076
+
Steptoe/Morex(BxF)
+
AD_SCRI_112.CEL
+
+
+
OK
+
+
+
+
58
+
SM077
+
2907077
+
Morex/Steptoe(CxF)
+
AD_SCRI_142.CEL
+
+
+
OK
+
+
+
+
59
+
SM078
+
2907078
+
Steptoe/Morex(BxF)
+
AD_SCRI_86.CEL
+
+
+
OK
+
+
+
+
60
+
SM079
+
2907079
+
Morex/Steptoe(CxF)
+
AD_SCRI_153.CEL
+
0521-16_SetA16.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
61
+
SM080
+
2907080
+
Steptoe/Morex(BxF)
+
AD_SCRI_107.CEL
+
+
+
OK
+
+
+
+
62
+
SM081
+
2907081
+
Morex/Steptoe(CxF)
+
AD_SCRI_105.CEL
+
+
+
OK
+
+
+
+
63
+
SM082
+
2907082
+
Steptoe/Morex(BxF)
+
AD_SCRI_97.CEL
+
+
+
OK
+
+
+
+
64
+
SM083
+
2907083
+
Steptoe/Morex(BxF)
+
AD_SCRI_89.CEL
+
+
+
OK
+
+
+
+
65
+
SM084
+
2907084
+
Morex/Steptoe(CxF)
+
AD_SCRI_155.CEL
+
+
+
OK
+
+
+
+
66
+
SM085
+
2907085
+
Morex/Steptoe(IxE)
+
AD_SCRI_149.CEL
+
0521-17_SetA17.CEL
+
SMmini
+
OK
+
OK
+
+
+
67
+
SM087
+
2907087
+
Steptoe/Morex(OxJ)
+
AD_SCRI_113.CEL
+
+
+
OK
+
+
+
+
68
+
SM088
+
2907088
+
Morex/Steptoe(CxF)
+
AD_SCRI_93.CEL
+
0521-18_SetA18.CEL
+
SMmini
+
OK
+
OK
+
+
+
69
+
SM089
+
2907089
+
Steptoe/Morex(OxJ)
+
AD_SCRI_148.CEL
+
0521-19_SetA19.CEL
+
SMmini
+
OK
+
OK
+
+
+
70
+
SM091
+
2907091
+
Morex/Steptoe(CxF)
+
AD_SCRI_110.CEL
+
+
+
OK
+
+
+
+
71
+
SM092
+
2907092
+
Steptoe/Morex(OxJ)
+
AD_SCRI_7.CEL
+
+
+
OK
+
+
+
+
72
+
SM093
+
2907093
+
Steptoe/Morex(BxF)
+
AD_SCRI_122.CEL
+
+
+
OK
+
+
+
+
73
+
SM094
+
2907094
+
Morex/Steptoe(CxF)
+
AD_SCRI_150.CEL
+
+
+
OK
+
+
+
+
74
+
SM097
+
2907097
+
Morex/Steptoe(CxF)
+
AD_SCRI_158.CEL
+
+
+
OK
+
+
+
+
75
+
SM098
+
2907098
+
Morex/Steptoe(CxF)
+
AD_SCRI_121.CEL
+
+
+
OK
+
+
+
+
76
+
SM099
+
2907099
+
Steptoe/Morex(QxG)
+
AD_SCRI_137.CEL
+
+
+
OK
+
+
+
+
77
+
SM103
+
2907103
+
Morex/Steptoe(IxE)
+
AD_SCRI_156.CEL
+
+
+
OK
+
+
+
+
78
+
SM104
+
2907104
+
Steptoe/Morex(BxH)
+
AD_SCRI_70.CEL
+
+
+
ERROR
+
+
+
+
79
+
SM105
+
2907105
+
Morex/Steptoe(IxE)
+
AD_SCRI_69.CEL
+
+
+
OK
+
+
+
+
80
+
SM110
+
2907110
+
Morex/Steptoe(CxF)
+
AD_SCRI_75.CEL
+
+
+
ERROR
+
+
+
+
81
+
SM112
+
2907112
+
Steptoe/Morex(BxF)
+
AD_SCRI_84.CEL
+
+
+
OK
+
+
+
+
82
+
SM116
+
2907116
+
Morex/Steptoe(CxF)
+
AD_SCRI_117.CEL
+
0521-20_SetA20.CEL
+
SMmini
+
OK
+
OK
+
+
+
83
+
SM120
+
2907120
+
Steptoe/Morex(OxJ)
+
AD_SCRI_138.CEL
+
+
+
OK
+
+
+
+
84
+
SM124
+
2907124
+
Steptoe/Morex(BxF)
+
AD_SCRI_146.CEL
+
+
+
OK
+
+
+
+
85
+
SM125
+
2907125
+
Morex/Steptoe(IxE)
+
AD_SCRI_43.CEL
+
+
+
OK
+
+
+
+
86
+
SM126
+
2907126
+
Steptoe/Morex(OxJ)
+
AD_SCRI_144_redo.CEL
+
+
+
OK
+
+
+
+
87
+
SM127
+
2907127
+
Steptoe/Morex(BxH)
+
AD_SCRI_129.CEL
+
+
+
OK
+
+
+
+
88
+
SM129
+
2907129
+
Steptoe/Morex(OxJ)
+
AD_SCRI_132.CEL
+
+
+
OK
+
+
+
+
89
+
SM130
+
2907130
+
Morex/Steptoe(CxF)
+
AD_SCRI_101.CEL
+
0521-21_SetA21.CEL
+
SMmini
+
OK
+
OK
+
+
+
90
+
SM131
+
2907131
+
Steptoe/Morex(OxJ)
+
AD_SCRI_102.CEL
+
+
+
OK
+
+
+
+
91
+
SM132
+
2907132
+
Steptoe/Morex(QxG)
+
AD_SCRI_4_redo.CEL
+
+
+
OK
+
+
+
+
92
+
SM133
+
2907133
+
Morex/Steptoe(CxF)
+
AD_SCRI_157.CEL
+
+
+
OK
+
+
+
+
93
+
SM134
+
2907134
+
Morex/Steptoe(IxE)
+
AD_SCRI_159.CEL
+
+
+
OK
+
+
+
+
94
+
SM135
+
2907135
+
Steptoe/Morex(BxF)
+
AD_SCRI_72.CEL
+
0521-22_SetA22.CEL
+
SMmini
+
OK
+
OK
+
+
+
95
+
SM136
+
2907136
+
Steptoe/Morex(QxG)
+
AD_SCRI_123.CEL
+
0521-23_SetA23.CEL
+
SMmini
+
OK
+
OK
+
+
+
96
+
SM137
+
2907137
+
Steptoe/Morex(BxH)
+
AD_SCRI_39.CEL
+
+
+
OK
+
+
+
+
97
+
SM139
+
2907139
+
Morex/Steptoe(CxF)
+
AD_SCRI_133.CEL
+
+
+
OK
+
+
+
+
98
+
SM140
+
2907140
+
Morex/Steptoe(CxF)
+
AD_SCRI_134.CEL
+
0521-24_SetA24.CEL
+
SMmini
+
OK
+
OK
+
+
+
99
+
SM141
+
2907141
+
Steptoe/Morex(BxH)
+
AD_SCRI_136.CEL
+
0521-25_SetA25.CEL
+
SMmini
+
OK
+
OK
+
+
+
100
+
SM142
+
2907142
+
Morex/Steptoe(IxE)
+
AD_SCRI_6.CEL
+
+
+
OK
+
+
+
+
101
+
SM143
+
2907143
+
Steptoe/Morex(BxH)
+
AD_SCRI_145.CEL
+
+
+
OK
+
+
+
+
102
+
SM144
+
2907144
+
Steptoe/Morex(BxF)
+
AD_SCRI_103.CEL
+
+
+
OK
+
+
+
+
103
+
SM145
+
2907145
+
Steptoe/Morex(QxG)
+
AD_SCRI_108.CEL
+
+
+
OK
+
+
+
+
104
+
SM146
+
2907146
+
Morex/Steptoe(BxF)
+
AD_SCRI_91.CEL
+
0521-26_SetA26.CEL
+
SMmini
+
OK
+
OK
+
+
+
105
+
SM147
+
2907147
+
Steptoe/Morex(OxJ)
+
AD_SCRI_139.CEL
+
+
+
OK
+
+
+
+
106
+
SM149
+
2907149
+
Steptoe/Morex(BxF)
+
AD_SCRI_131.CEL
+
+
+
ERROR
+
+
+
+
107
+
SM150
+
2907150
+
Morex/Steptoe(CxF)
+
AD_SCRI_37.CEL
+
+
+
OK
+
+
+
+
108
+
SM151
+
2907151
+
Morex/Steptoe(IxE)
+
AD_SCRI_28.CEL
+
+
+
OK
+
+
+
+
109
+
SM152
+
2907152
+
Steptoe/Morex(BxH)
+
AD_SCRI_9_redo.CEL
+
0521-27_SetA27.CEL
+
SMmini
+
OK
+
OK
+
+
+
110
+
SM153
+
2907153
+
Steptoe/Morex(BxH)
+
AD_SCRI_135.CEL
+
+
+
OK
+
+
+
+
111
+
SM154
+
2907154
+
Steptoe/Morex(BxH)
+
AD_SCRI_114.CEL
+
+
+
OK
+
+
+
+
112
+
SM155
+
2907155
+
Steptoe/Morex(BxH)
+
AD_SCRI_119.CEL
+
0521-28_SetA28.CEL
+
SMmini
+
OK
+
OK
+
+
+
113
+
SM156
+
2907156
+
Steptoe/Morex(BxH)
+
AD_SCRI_140.CEL
+
+
+
OK
+
+
+
+
114
+
SM157
+
2907157
+
Morex/Steptoe(CxF)
+
AD_SCRI_106_redo.CEL
+
+
+
OK
+
+
+
+
115
+
SM158
+
2907158
+
Morex/Steptoe(CxF)
+
AD_SCRI_65.CEL
+
+
+
OK
+
+
+
+
116
+
SM159
+
2907159
+
Morex/Steptoe(IxE)
+
AD_SCRI_168.CEL
+
+
+
OK
+
+
+
+
117
+
SM160
+
2907160
+
Steptoe/Morex(OxJ)
+
AD_SCRI_47.CEL
+
0521-29_SetA29.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
118
+
SM161
+
2907161
+
Steptoe/Morex(BxH)
+
AD_SCRI_76.CEL
+
+
+
ERROR
+
+
+
+
119
+
SM162
+
2907162
+
Morex/Steptoe(CxF)
+
AD_SCRI_147.CEL
+
+
+
OK
+
+
+
+
120
+
SM164
+
2907164
+
Steptoe/Morex(OxJ)
+
AD_SCRI_128.CEL
+
+
+
OK
+
+
+
+
121
+
SM165
+
2907165
+
Steptoe/Morex(BxH)
+
AD_SCRI_143.CEL
+
+
+
OK
+
OK
+
+
+
122
+
SM166
+
2907166
+
Morex/Steptoe(CxF)
+
AD_SCRI_115.CEL
+
+
+
OK
+
+
+
+
123
+
SM167
+
2907167
+
Steptoe/Morex(BxH)
+
AD_SCRI_127.CEL
+
0521-30_SetA30.CEL
+
SMmini
+
OK
+
OK
+
+
+
124
+
SM168
+
2907168
+
Steptoe/Morex(BxH)
+
AD_SCRI_130.CEL
+
+
+
OK
+
+
+
+
125
+
SM169
+
2907169
+
Morex/Steptoe(CxF)
+
AD_SCRI_118.CEL
+
0521-31_SetA31.CEL
+
SMmini
+
OK
+
OK
+
+
+
126
+
SM170
+
2907170
+
Steptoe/Morex(BxF)
+
AD_SCRI_151.CEL
+
+
+
OK
+
+
+
+
127
+
SM171
+
2907171
+
Steptoe/Morex(BxF)
+
AD_SCRI_165.CEL
+
+
+
ERROR
+
+
+
+
128
+
SM172
+
2907172
+
Steptoe/Morex(OxJ)
+
AD_SCRI_152.CEL
+
+
+
ERROR
+
+
+
+
129
+
SM173
+
2907173
+
Steptoe/Morex(OxJ)
+
AD_SCRI_104.CEL
+
0521-32_SetA32.CEL
+
SMmini
+
OK
+
OK
+
+
+
130
+
SM174
+
2907174
+
Steptoe/Morex(BxH)
+
AD_SCRI_154.CEL
+
+
+
OK
+
+
+
+
131
+
SM176
+
2907176
+
Morex/Steptoe(CxF)
+
AD_SCRI_141.CEL
+
+
+
OK
+
+
+
+
132
+
SM177
+
2907177
+
Morex/Steptoe(CxF)
+
AD_SCRI_111.CEL
+
0521-33_SetA33.CEL
+
SMmini
+
OK
+
OK
+
+
+
133
+
SM179
+
2907179
+
Morex/Steptoe(CxF)
+
AD_SCRI_166.CEL
+
+
+
OK
+
+
+
+
134
+
SM180
+
2907180
+
Morex/Steptoe(IxE)
+
AD_SCRI_161.CEL
+
+
+
OK
+
+
+
+
135
+
SM181
+
2907181
+
Morex/Steptoe(IxE)
+
AD_SCRI_162.CEL
+
+
+
OK
+
+
+
+
136
+
SM182
+
2907182
+
Morex/Steptoe(CxF)
+
AD_SCRI_163.CEL
+
+
+
OK
+
+
+
+
137
+
SM183
+
2907183
+
Morex/Steptoe(CxF)
+
AD_SCRI_164.CEL
+
+
+
OK
+
+
+
+
138
+
SM184
+
2907184
+
Morex/Steptoe(IxE)
+
AD_SCRI_160.CEL
+
0521-34_SetA34.CEL
+
SMmini
+
OK
+
OK
+
+
+
139
+
SM185
+
2907185
+
Morex/Steptoe(IxE)
+
AD_SCRI_167.CEL
+
+
+
OK
+
+
+
+
140
+
SM186
+
2907186
+
Morex/Steptoe(IxE)
+
AD_SCRI_62.CEL
+
+
+
OK
+
+
+
+
141
+
SM187
+
2907187
+
Morex/Steptoe(IxE)
+
AD_SCRI_61.CEL
+
+
+
OK
+
+
+
+
142
+
SM188
+
2907188
+
Morex/Steptoe(CxF)
+
AD_SCRI_63.CEL
+
+
+
OK
+
+
+
+
143
+
SM189
+
2907189
+
Steptoe/Morex(QxG)
+
AD_SCRI_80.CEL
+
+
+
OK
+
+
+
+
144
+
SM193
+
2907193
+
Morex/Steptoe(IxE)
+
AD_SCRI_36.CEL
+
+
+
OK
+
+
+
+
145
+
SM194
+
2907194
+
Steptoe/Morex(OxJ)
+
AD_SCRI_29.CEL
+
+
+
OK
+
+
+
+
146
+
SM196
+
2907196
+
Steptoe/Morex(BxF)
+
AD_SCRI_26.CEL
+
+
+
OK
+
+
+
+
147
+
SM197
+
2907197
+
Steptoe/Morex(BxF)
+
AD_SCRI_85.CEL
+
+
+
OK
+
+
+
+
148
+
SM198
+
2907198
+
Morex/Steptoe(IxE)
+
AD_SCRI_8.CEL
+
+
+
OK
+
+
+
+
149
+
SM199
+
2907199
+
Steptoe/Morex(BxF)
+
AD_SCRI_20.CEL
+
+
+
OK
+
+
+
+
150
+
SM200
+
2907200
+
Morex/Steptoe(IxE)
+
AD_SCRI_38.CEL
+
0521-35_SetA35.CEL
+
SMmini
+
OK
+
OK
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_17.CEL
+
0521-36_SetA36.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_66.CEL
+
0521-37_SetA37.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_68.CEL
+
0521-38_SetA38.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_116.CEL
+
0521-39_SetA39.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_14.CEL
+
0521-40_SetA40.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_67.CEL
+
0521-41_SetA41.CEL
+
+
+
+
+
+
+
+
+
About tissues used to generate this set of data:
+
+
+
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
+
+
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
+
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
+
+
+
+
+
+
RNA Sample Processing:
+
Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
+
+☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
+☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
+☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
+☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
+☐ While centrifuging, label new set of 15 ml tubes
+☐ Transfer supernatant to 15 ml centrifuge tube
+☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
+seconds, and incubate at room temperature for 5 minutes.
+☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
+☐ While centrifuging, label new 15 ml tubes
+☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
+☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
+☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
+☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
+4000 rpm for 15 minutes @ 4oC.
+☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
+☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
+☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
+few times.
+☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
+☐ Set water bath to 37oC.
+☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
+☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
+☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
+☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
+☐ Label 15 ml tubes from the kit and place midi columns in them
+☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
+☐ Discard the flow-through.
+☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
+incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
+☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
+gently, incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
+☐ Centrifuge again for another 5 min.
+☐ Label new 15 ml tubes from the kit.
+☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
+RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ To the same tube add again 250 ul H2O, incubate for 1 min.
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ Label two sets of 1.5 ml Eppendorf tubes.
+☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
+
+
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
+
+
Replication and Sample Balance:
+
3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
+
Experimental Design and Batch Structure:
+
+
+
+
+
+
Downloading complete data set:
+
+
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
+E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
+
+
+
+
About the array platform:
+
+
+
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
+
+
The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
+
+
+
+
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
+Barley1 Leaf MAS 5.0 SCRI (Dec 06)
+
+
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
+
+
+
Values below 0.01 were set to 0.01.
+
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
+
Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
+
+
+
+
+
+
+
+
Data source acknowledgment:
+
+
+
Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant
+
+
+SCR/910/04
+
+'The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
+
+
+
Contact address:
+
+
Arnis Druka
+
+Genetics Programme
+
+Scottish Crop Research Institute
+
+Invergowrie, Dundee DD2 5DA
+
+Angus, Scotland, United Kingdom
+
+Tel +44 01382 562731
+Fax +44 01382 568587
+adruka@scri.sari.ac.uk
+
+
+
References:
+
+
+
Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics, Jul;6(3):202-11.
+
+
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
+
+
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
+
+
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
+
+
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
+
+
+
+
+
+
+
About this text file:
+
+
+This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
Barley1 Embryo gcRMA SCRI (Dec 06) - integrated probe set value for each gene has been calculated using RMA algorithm (Irizarry et al 2003). RMA ignores MM probe signals. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
+
+
+
+
+
Summary:
+
+
+
The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip (GEO GPL1340). For updated annotation of the Barley1 22k array see PLEXdb.
+
+
+
+
About the lines used to generate this set of data:
+
+
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
+
+
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
+1)
+pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
+2)
+'minimapper' subset - MINI;
+3) lines that have expression data removed - ERROR:
+
+
+
+
Order #
+
Line ID
+
Permanent Oregon ID
+
Cross direction
+
CEL file names
+
Mini-mapper set
+
Error check
+
+
+
embryo data-set
+
leaf data-set
+
embryo data-set
+
leaf data-set
+
+
+
1
+
SM001
+
2907001
+
Steptoe/Morex(BxF)
+
AD_SCRI_82.CEL
+
+
+
OK
+
+
+
+
2
+
SM002
+
2907002
+
Steptoe/Morex(BxF)
+
AD_SCRI_1.CEL
+
+
+
OK
+
+
+
+
3
+
SM003
+
2907003
+
Morex/Steptoe(CxF)
+
AD_SCRI_19.CEL
+
+
+
OK
+
+
+
+
4
+
SM004
+
2907004
+
Morex/Steptoe(CxF)
+
AD_SCRI_3.CEL
+
0521-1_SetA1.CEL
+
SMmini
+
OK
+
OK
+
+
+
5
+
SM005
+
2907005
+
Steptoe/Morex(BxH)
+
AD_SCRI_88.CEL
+
+
+
OK
+
+
+
+
6
+
SM006
+
2907006
+
Morex/Steptoe(CxF)
+
AD_SCRI_48.CEL
+
+
+
OK
+
+
+
+
7
+
SM007
+
2907007
+
Steptoe/Morex(BxH)
+
AD_SCRI_35.CEL
+
0521-2_SetA2.CEL
+
SMmini
+
OK
+
OK
+
+
+
8
+
SM009
+
2907009
+
Steptoe/Morex(BxF)
+
AD_SCRI_2.CEL
+
+
+
OK
+
+
+
+
9
+
SM010
+
2907010
+
Morex/Steptoe(IxE)
+
AD_SCRI_42.CEL
+
+
+
OK
+
+
+
+
10
+
SM011
+
2907011
+
Steptoe/Morex(QxG)
+
AD_SCRI_10.CEL
+
+
+
OK
+
+
+
+
11
+
SM012
+
2907012
+
Morex/Steptoe(CxF)
+
AD_SCRI_45.CEL
+
0521-3_SetA3.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
12
+
SM013
+
2907013
+
Morex/Steptoe(IxE)
+
AD_SCRI_78.CEL
+
0521-4_SetA4.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
13
+
SM014
+
2907014
+
Steptoe/Morex(BxH)
+
AD_SCRI_18.CEL
+
+
+
OK
+
+
+
+
14
+
SM015
+
2907015
+
Steptoe/Morex(BxH)
+
AD_SCRI_5.CEL
+
+
+
OK
+
+
+
+
15
+
SM016
+
2907016
+
Steptoe/Morex(BxH)
+
AD_SCRI_21.CEL
+
+
+
OK
+
+
+
+
16
+
SM020
+
2907020
+
Steptoe/Morex(OxJ)
+
AD_SCRI_77.CEL
+
+
+
OK
+
+
+
+
17
+
SM021
+
2907021
+
Morex/Steptoe(IxE)
+
AD_SCRI_30.CEL
+
+
+
OK
+
+
+
+
18
+
SM022
+
2907022
+
Morex/Steptoe(IxE)
+
AD_SCRI_31.CEL
+
0521-5_SetA5.CEL
+
SMmini
+
OK
+
OK
+
+
+
19
+
SM023
+
2907023
+
Steptoe/Morex(BxH)
+
AD_SCRI_32.CEL
+
+
+
OK
+
+
+
+
20
+
SM024
+
2907024
+
Morex/Steptoe(IxE)
+
AD_SCRI_33.CEL
+
0521-6_SetA6.CEL
+
SMmini
+
OK
+
OK
+
+
+
21
+
SM025
+
2907025
+
Morex/Steptoe(CxF)
+
AD_SCRI_34.CEL
+
+
+
OK
+
+
+
+
22
+
SM027
+
2907027
+
Steptoe/Morex(OxJ)
+
AD_SCRI_12.CEL
+
0521-7_SetA7.CEL
+
SMmini
+
OK
+
OK
+
+
+
23
+
SM030
+
2907030
+
Morex/Steptoe(IxE)
+
AD_SCRI_79.CEL
+
+
+
OK
+
+
+
+
24
+
SM031
+
2907031
+
Steptoe/Morex(OxJ)
+
AD_SCRI_16.CEL
+
+
+
OK
+
+
+
+
25
+
SM032
+
2907032
+
Morex/Steptoe(IxE)
+
AD_SCRI_13.CEL
+
+
+
OK
+
+
+
+
26
+
SM035
+
2907035
+
Morex/Steptoe(CxF)
+
AD_SCRI_15.CEL
+
+
+
ERROR
+
+
+
+
27
+
SM039
+
2907039
+
Morex/Steptoe(CxF)
+
AD_SCRI_41.CEL
+
+
+
OK
+
+
+
+
28
+
SM040
+
2907040
+
Steptoe/Morex(BxH)
+
AD_SCRI_83.CEL
+
+
+
OK
+
+
+
+
29
+
SM041
+
2907041
+
Steptoe/Morex(OxJ)
+
AD_SCRI_11_redo.CEL
+
0521-8_SetA8.CEL
+
SMmini
+
OK
+
OK
+
+
+
30
+
SM042
+
2907042
+
Morex/Steptoe(CxF)
+
AD_SCRI_57.CEL
+
+
+
OK
+
+
+
+
31
+
SM043
+
2907043
+
Morex/Steptoe(JxE)
+
AD_SCRI_49.CEL
+
0521-9_SetA9.CEL
+
SMmini
+
OK
+
OK
+
+
+
32
+
SM044
+
2907044
+
Steptoe/Morex(OxJ)
+
AD_SCRI_50.CEL
+
0521-10_SetA10.CEL
+
SMmini
+
OK
+
OK
+
+
+
33
+
SM045
+
2907045
+
Steptoe/Morex(BxH)
+
AD_SCRI_51.CEL
+
+
+
OK
+
+
+
+
34
+
SM046
+
2907046
+
Steptoe/Morex(OxJ)
+
AD_SCRI_52.CEL
+
0521-11_SetA11.CEL
+
SMmini
+
OK
+
OK
+
+
+
35
+
SM048
+
2907048
+
Steptoe/Morex(BxF)
+
AD_SCRI_53.CEL
+
+
+
ERROR
+
+
+
+
36
+
SM050
+
2907050
+
Morex/Steptoe(IxE)
+
AD_SCRI_46.CEL
+
+
+
OK
+
+
+
+
37
+
SM054
+
2907054
+
Morex/Steptoe(CxF)
+
AD_SCRI_60.CEL
+
+
+
OK
+
+
+
+
38
+
SM055
+
2907055
+
Steptoe/Morex(OxJ)
+
AD_SCRI_55.CEL
+
+
+
OK
+
+
+
+
39
+
SM056
+
2907056
+
Steptoe/Morex(BxH)
+
AD_SCRI_23.CEL
+
+
+
OK
+
+
+
+
40
+
SM057
+
2907057
+
Morex/Steptoe(CxF)
+
AD_SCRI_24.CEL
+
+
+
OK
+
+
+
+
41
+
SM058
+
2907058
+
Steptoe/Morex(BxF)
+
AD_SCRI_22.CEL
+
+
+
OK
+
+
+
+
42
+
SM059
+
2907059
+
Steptoe/Morex(BxH)
+
AD_SCRI_27.CEL
+
+
+
OK
+
+
+
+
43
+
SM061
+
2907061
+
Morex/Steptoe(LxF)
+
AD_SCRI_81.CEL
+
0521-12_SetA12.CEL
+
SMmini
+
OK
+
OK
+
+
+
44
+
SM062
+
2907062
+
Morex/Steptoe(CxF)
+
AD_SCRI_44.CEL
+
+
+
OK
+
+
+
+
45
+
SM063
+
2907063
+
Steptoe/Morex(OxJ)
+
AD_SCRI_40.CEL
+
0521-13_SetA13.CEL
+
SMmini
+
OK
+
OK
+
+
+
46
+
SM064
+
2907064
+
Morex/Steptoe(CxF)
+
AD_SCRI_87_redo.CEL
+
+
+
OK
+
+
+
+
47
+
SM065
+
2907065
+
Morex/Steptoe(CxF)
+
AD_SCRI_54.CEL
+
+
+
OK
+
+
+
+
48
+
SM067
+
2907067
+
Steptoe/Morex(OxJ)
+
AD_SCRI_73.CEL
+
+
+
OK
+
+
+
+
49
+
SM068
+
2907068
+
Steptoe/Morex(OxG)
+
AD_SCRI_56.CEL
+
+
+
ERROR
+
+
+
+
50
+
SM069
+
2907069
+
Steptoe/Morex(BxH)
+
AD_SCRI_71.CEL
+
+
+
OK
+
+
+
+
51
+
SM070
+
2907070
+
Steptoe/Morex(BxF)
+
AD_SCRI_64.CEL
+
+
+
OK
+
+
+
+
52
+
SM071
+
2907071
+
Steptoe/Morex(BxH)
+
AD_SCRI_58.CEL
+
+
+
OK
+
+
+
+
53
+
SM072
+
2907072
+
Morex/Steptoe(CxF)
+
AD_SCRI_59.CEL
+
+
+
OK
+
+
+
+
54
+
SM073
+
2907073
+
Steptoe/Morex(BxF)
+
AD_SCRI_74.CEL
+
0521-14_SetA14.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
55
+
SM074
+
2907074
+
Morex/Steptoe(CxF)
+
AD_SCRI_25.CEL
+
0521-15_SetA15.CEL
+
SMmini
+
OK
+
OK
+
+
+
56
+
SM075
+
2907075
+
Steptoe/Morex(QxG)
+
AD_SCRI_120.CEL
+
+
+
OK
+
+
+
+
57
+
SM076
+
2907076
+
Steptoe/Morex(BxF)
+
AD_SCRI_112.CEL
+
+
+
OK
+
+
+
+
58
+
SM077
+
2907077
+
Morex/Steptoe(CxF)
+
AD_SCRI_142.CEL
+
+
+
OK
+
+
+
+
59
+
SM078
+
2907078
+
Steptoe/Morex(BxF)
+
AD_SCRI_86.CEL
+
+
+
OK
+
+
+
+
60
+
SM079
+
2907079
+
Morex/Steptoe(CxF)
+
AD_SCRI_153.CEL
+
0521-16_SetA16.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
61
+
SM080
+
2907080
+
Steptoe/Morex(BxF)
+
AD_SCRI_107.CEL
+
+
+
OK
+
+
+
+
62
+
SM081
+
2907081
+
Morex/Steptoe(CxF)
+
AD_SCRI_105.CEL
+
+
+
OK
+
+
+
+
63
+
SM082
+
2907082
+
Steptoe/Morex(BxF)
+
AD_SCRI_97.CEL
+
+
+
OK
+
+
+
+
64
+
SM083
+
2907083
+
Steptoe/Morex(BxF)
+
AD_SCRI_89.CEL
+
+
+
OK
+
+
+
+
65
+
SM084
+
2907084
+
Morex/Steptoe(CxF)
+
AD_SCRI_155.CEL
+
+
+
OK
+
+
+
+
66
+
SM085
+
2907085
+
Morex/Steptoe(IxE)
+
AD_SCRI_149.CEL
+
0521-17_SetA17.CEL
+
SMmini
+
OK
+
OK
+
+
+
67
+
SM087
+
2907087
+
Steptoe/Morex(OxJ)
+
AD_SCRI_113.CEL
+
+
+
OK
+
+
+
+
68
+
SM088
+
2907088
+
Morex/Steptoe(CxF)
+
AD_SCRI_93.CEL
+
0521-18_SetA18.CEL
+
SMmini
+
OK
+
OK
+
+
+
69
+
SM089
+
2907089
+
Steptoe/Morex(OxJ)
+
AD_SCRI_148.CEL
+
0521-19_SetA19.CEL
+
SMmini
+
OK
+
OK
+
+
+
70
+
SM091
+
2907091
+
Morex/Steptoe(CxF)
+
AD_SCRI_110.CEL
+
+
+
OK
+
+
+
+
71
+
SM092
+
2907092
+
Steptoe/Morex(OxJ)
+
AD_SCRI_7.CEL
+
+
+
OK
+
+
+
+
72
+
SM093
+
2907093
+
Steptoe/Morex(BxF)
+
AD_SCRI_122.CEL
+
+
+
OK
+
+
+
+
73
+
SM094
+
2907094
+
Morex/Steptoe(CxF)
+
AD_SCRI_150.CEL
+
+
+
OK
+
+
+
+
74
+
SM097
+
2907097
+
Morex/Steptoe(CxF)
+
AD_SCRI_158.CEL
+
+
+
OK
+
+
+
+
75
+
SM098
+
2907098
+
Morex/Steptoe(CxF)
+
AD_SCRI_121.CEL
+
+
+
OK
+
+
+
+
76
+
SM099
+
2907099
+
Steptoe/Morex(QxG)
+
AD_SCRI_137.CEL
+
+
+
OK
+
+
+
+
77
+
SM103
+
2907103
+
Morex/Steptoe(IxE)
+
AD_SCRI_156.CEL
+
+
+
OK
+
+
+
+
78
+
SM104
+
2907104
+
Steptoe/Morex(BxH)
+
AD_SCRI_70.CEL
+
+
+
ERROR
+
+
+
+
79
+
SM105
+
2907105
+
Morex/Steptoe(IxE)
+
AD_SCRI_69.CEL
+
+
+
OK
+
+
+
+
80
+
SM110
+
2907110
+
Morex/Steptoe(CxF)
+
AD_SCRI_75.CEL
+
+
+
ERROR
+
+
+
+
81
+
SM112
+
2907112
+
Steptoe/Morex(BxF)
+
AD_SCRI_84.CEL
+
+
+
OK
+
+
+
+
82
+
SM116
+
2907116
+
Morex/Steptoe(CxF)
+
AD_SCRI_117.CEL
+
0521-20_SetA20.CEL
+
SMmini
+
OK
+
OK
+
+
+
83
+
SM120
+
2907120
+
Steptoe/Morex(OxJ)
+
AD_SCRI_138.CEL
+
+
+
OK
+
+
+
+
84
+
SM124
+
2907124
+
Steptoe/Morex(BxF)
+
AD_SCRI_146.CEL
+
+
+
OK
+
+
+
+
85
+
SM125
+
2907125
+
Morex/Steptoe(IxE)
+
AD_SCRI_43.CEL
+
+
+
OK
+
+
+
+
86
+
SM126
+
2907126
+
Steptoe/Morex(OxJ)
+
AD_SCRI_144_redo.CEL
+
+
+
OK
+
+
+
+
87
+
SM127
+
2907127
+
Steptoe/Morex(BxH)
+
AD_SCRI_129.CEL
+
+
+
OK
+
+
+
+
88
+
SM129
+
2907129
+
Steptoe/Morex(OxJ)
+
AD_SCRI_132.CEL
+
+
+
OK
+
+
+
+
89
+
SM130
+
2907130
+
Morex/Steptoe(CxF)
+
AD_SCRI_101.CEL
+
0521-21_SetA21.CEL
+
SMmini
+
OK
+
OK
+
+
+
90
+
SM131
+
2907131
+
Steptoe/Morex(OxJ)
+
AD_SCRI_102.CEL
+
+
+
OK
+
+
+
+
91
+
SM132
+
2907132
+
Steptoe/Morex(QxG)
+
AD_SCRI_4_redo.CEL
+
+
+
OK
+
+
+
+
92
+
SM133
+
2907133
+
Morex/Steptoe(CxF)
+
AD_SCRI_157.CEL
+
+
+
OK
+
+
+
+
93
+
SM134
+
2907134
+
Morex/Steptoe(IxE)
+
AD_SCRI_159.CEL
+
+
+
OK
+
+
+
+
94
+
SM135
+
2907135
+
Steptoe/Morex(BxF)
+
AD_SCRI_72.CEL
+
0521-22_SetA22.CEL
+
SMmini
+
OK
+
OK
+
+
+
95
+
SM136
+
2907136
+
Steptoe/Morex(QxG)
+
AD_SCRI_123.CEL
+
0521-23_SetA23.CEL
+
SMmini
+
OK
+
OK
+
+
+
96
+
SM137
+
2907137
+
Steptoe/Morex(BxH)
+
AD_SCRI_39.CEL
+
+
+
OK
+
+
+
+
97
+
SM139
+
2907139
+
Morex/Steptoe(CxF)
+
AD_SCRI_133.CEL
+
+
+
OK
+
+
+
+
98
+
SM140
+
2907140
+
Morex/Steptoe(CxF)
+
AD_SCRI_134.CEL
+
0521-24_SetA24.CEL
+
SMmini
+
OK
+
OK
+
+
+
99
+
SM141
+
2907141
+
Steptoe/Morex(BxH)
+
AD_SCRI_136.CEL
+
0521-25_SetA25.CEL
+
SMmini
+
OK
+
OK
+
+
+
100
+
SM142
+
2907142
+
Morex/Steptoe(IxE)
+
AD_SCRI_6.CEL
+
+
+
OK
+
+
+
+
101
+
SM143
+
2907143
+
Steptoe/Morex(BxH)
+
AD_SCRI_145.CEL
+
+
+
OK
+
+
+
+
102
+
SM144
+
2907144
+
Steptoe/Morex(BxF)
+
AD_SCRI_103.CEL
+
+
+
OK
+
+
+
+
103
+
SM145
+
2907145
+
Steptoe/Morex(QxG)
+
AD_SCRI_108.CEL
+
+
+
OK
+
+
+
+
104
+
SM146
+
2907146
+
Morex/Steptoe(BxF)
+
AD_SCRI_91.CEL
+
0521-26_SetA26.CEL
+
SMmini
+
OK
+
OK
+
+
+
105
+
SM147
+
2907147
+
Steptoe/Morex(OxJ)
+
AD_SCRI_139.CEL
+
+
+
OK
+
+
+
+
106
+
SM149
+
2907149
+
Steptoe/Morex(BxF)
+
AD_SCRI_131.CEL
+
+
+
ERROR
+
+
+
+
107
+
SM150
+
2907150
+
Morex/Steptoe(CxF)
+
AD_SCRI_37.CEL
+
+
+
OK
+
+
+
+
108
+
SM151
+
2907151
+
Morex/Steptoe(IxE)
+
AD_SCRI_28.CEL
+
+
+
OK
+
+
+
+
109
+
SM152
+
2907152
+
Steptoe/Morex(BxH)
+
AD_SCRI_9_redo.CEL
+
0521-27_SetA27.CEL
+
SMmini
+
OK
+
OK
+
+
+
110
+
SM153
+
2907153
+
Steptoe/Morex(BxH)
+
AD_SCRI_135.CEL
+
+
+
OK
+
+
+
+
111
+
SM154
+
2907154
+
Steptoe/Morex(BxH)
+
AD_SCRI_114.CEL
+
+
+
OK
+
+
+
+
112
+
SM155
+
2907155
+
Steptoe/Morex(BxH)
+
AD_SCRI_119.CEL
+
0521-28_SetA28.CEL
+
SMmini
+
OK
+
OK
+
+
+
113
+
SM156
+
2907156
+
Steptoe/Morex(BxH)
+
AD_SCRI_140.CEL
+
+
+
OK
+
+
+
+
114
+
SM157
+
2907157
+
Morex/Steptoe(CxF)
+
AD_SCRI_106_redo.CEL
+
+
+
OK
+
+
+
+
115
+
SM158
+
2907158
+
Morex/Steptoe(CxF)
+
AD_SCRI_65.CEL
+
+
+
OK
+
+
+
+
116
+
SM159
+
2907159
+
Morex/Steptoe(IxE)
+
AD_SCRI_168.CEL
+
+
+
OK
+
+
+
+
117
+
SM160
+
2907160
+
Steptoe/Morex(OxJ)
+
AD_SCRI_47.CEL
+
0521-29_SetA29.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
118
+
SM161
+
2907161
+
Steptoe/Morex(BxH)
+
AD_SCRI_76.CEL
+
+
+
ERROR
+
+
+
+
119
+
SM162
+
2907162
+
Morex/Steptoe(CxF)
+
AD_SCRI_147.CEL
+
+
+
OK
+
+
+
+
120
+
SM164
+
2907164
+
Steptoe/Morex(OxJ)
+
AD_SCRI_128.CEL
+
+
+
OK
+
+
+
+
121
+
SM165
+
2907165
+
Steptoe/Morex(BxH)
+
AD_SCRI_143.CEL
+
+
+
OK
+
OK
+
+
+
122
+
SM166
+
2907166
+
Morex/Steptoe(CxF)
+
AD_SCRI_115.CEL
+
+
+
OK
+
+
+
+
123
+
SM167
+
2907167
+
Steptoe/Morex(BxH)
+
AD_SCRI_127.CEL
+
0521-30_SetA30.CEL
+
SMmini
+
OK
+
OK
+
+
+
124
+
SM168
+
2907168
+
Steptoe/Morex(BxH)
+
AD_SCRI_130.CEL
+
+
+
OK
+
+
+
+
125
+
SM169
+
2907169
+
Morex/Steptoe(CxF)
+
AD_SCRI_118.CEL
+
0521-31_SetA31.CEL
+
SMmini
+
OK
+
OK
+
+
+
126
+
SM170
+
2907170
+
Steptoe/Morex(BxF)
+
AD_SCRI_151.CEL
+
+
+
OK
+
+
+
+
127
+
SM171
+
2907171
+
Steptoe/Morex(BxF)
+
AD_SCRI_165.CEL
+
+
+
ERROR
+
+
+
+
128
+
SM172
+
2907172
+
Steptoe/Morex(OxJ)
+
AD_SCRI_152.CEL
+
+
+
ERROR
+
+
+
+
129
+
SM173
+
2907173
+
Steptoe/Morex(OxJ)
+
AD_SCRI_104.CEL
+
0521-32_SetA32.CEL
+
SMmini
+
OK
+
OK
+
+
+
130
+
SM174
+
2907174
+
Steptoe/Morex(BxH)
+
AD_SCRI_154.CEL
+
+
+
OK
+
+
+
+
131
+
SM176
+
2907176
+
Morex/Steptoe(CxF)
+
AD_SCRI_141.CEL
+
+
+
OK
+
+
+
+
132
+
SM177
+
2907177
+
Morex/Steptoe(CxF)
+
AD_SCRI_111.CEL
+
0521-33_SetA33.CEL
+
SMmini
+
OK
+
OK
+
+
+
133
+
SM179
+
2907179
+
Morex/Steptoe(CxF)
+
AD_SCRI_166.CEL
+
+
+
OK
+
+
+
+
134
+
SM180
+
2907180
+
Morex/Steptoe(IxE)
+
AD_SCRI_161.CEL
+
+
+
OK
+
+
+
+
135
+
SM181
+
2907181
+
Morex/Steptoe(IxE)
+
AD_SCRI_162.CEL
+
+
+
OK
+
+
+
+
136
+
SM182
+
2907182
+
Morex/Steptoe(CxF)
+
AD_SCRI_163.CEL
+
+
+
OK
+
+
+
+
137
+
SM183
+
2907183
+
Morex/Steptoe(CxF)
+
AD_SCRI_164.CEL
+
+
+
OK
+
+
+
+
138
+
SM184
+
2907184
+
Morex/Steptoe(IxE)
+
AD_SCRI_160.CEL
+
0521-34_SetA34.CEL
+
SMmini
+
OK
+
OK
+
+
+
139
+
SM185
+
2907185
+
Morex/Steptoe(IxE)
+
AD_SCRI_167.CEL
+
+
+
OK
+
+
+
+
140
+
SM186
+
2907186
+
Morex/Steptoe(IxE)
+
AD_SCRI_62.CEL
+
+
+
OK
+
+
+
+
141
+
SM187
+
2907187
+
Morex/Steptoe(IxE)
+
AD_SCRI_61.CEL
+
+
+
OK
+
+
+
+
142
+
SM188
+
2907188
+
Morex/Steptoe(CxF)
+
AD_SCRI_63.CEL
+
+
+
OK
+
+
+
+
143
+
SM189
+
2907189
+
Steptoe/Morex(QxG)
+
AD_SCRI_80.CEL
+
+
+
OK
+
+
+
+
144
+
SM193
+
2907193
+
Morex/Steptoe(IxE)
+
AD_SCRI_36.CEL
+
+
+
OK
+
+
+
+
145
+
SM194
+
2907194
+
Steptoe/Morex(OxJ)
+
AD_SCRI_29.CEL
+
+
+
OK
+
+
+
+
146
+
SM196
+
2907196
+
Steptoe/Morex(BxF)
+
AD_SCRI_26.CEL
+
+
+
OK
+
+
+
+
147
+
SM197
+
2907197
+
Steptoe/Morex(BxF)
+
AD_SCRI_85.CEL
+
+
+
OK
+
+
+
+
148
+
SM198
+
2907198
+
Morex/Steptoe(IxE)
+
AD_SCRI_8.CEL
+
+
+
OK
+
+
+
+
149
+
SM199
+
2907199
+
Steptoe/Morex(BxF)
+
AD_SCRI_20.CEL
+
+
+
OK
+
+
+
+
150
+
SM200
+
2907200
+
Morex/Steptoe(IxE)
+
AD_SCRI_38.CEL
+
0521-35_SetA35.CEL
+
SMmini
+
OK
+
OK
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_17.CEL
+
0521-36_SetA36.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_66.CEL
+
0521-37_SetA37.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_68.CEL
+
0521-38_SetA38.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_116.CEL
+
0521-39_SetA39.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_14.CEL
+
0521-40_SetA40.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_67.CEL
+
0521-41_SetA41.CEL
+
+
+
+
+
+
+
+
+
About tissues used to generate this set of data:
+
+
+
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
+
+
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
+
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
+
+
+
+
+
+
RNA Sample Processing:
+
Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
+
+☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
+☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
+☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
+☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
+☐ While centrifuging, label new set of 15 ml tubes
+☐ Transfer supernatant to 15 ml centrifuge tube
+☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
+seconds, and incubate at room temperature for 5 minutes.
+☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
+☐ While centrifuging, label new 15 ml tubes
+☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
+☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
+☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
+☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
+4000 rpm for 15 minutes @ 4oC.
+☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
+☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
+☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
+few times.
+☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
+☐ Set water bath to 37oC.
+☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
+☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
+☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
+☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
+☐ Label 15 ml tubes from the kit and place midi columns in them
+☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
+☐ Discard the flow-through.
+☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
+incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
+☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
+gently, incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
+☐ Centrifuge again for another 5 min.
+☐ Label new 15 ml tubes from the kit.
+☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
+RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ To the same tube add again 250 ul H2O, incubate for 1 min.
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ Label two sets of 1.5 ml Eppendorf tubes.
+☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
+
+
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
+
+
Replication and Sample Balance:
+
3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
+
Experimental Design and Batch Structure:
+
+
+
+
+
+
Downloading complete data set:
+
+
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
+E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
+
+
+
+
About the array platform:
+
+
+
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
+
+
The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
+
+
+
+
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
+Barley1 Leaf MAS 5.0 SCRI (Dec 06)
+
+
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
+
+
+
Values below 0.01 were set to 0.01.
+
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
+
Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
+
+
+
+
+
+
+
+
Data source acknowledgment:
+
+
+
Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant
+
+
+SCR/910/04
+
+'The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
+
+
+
Contact address:
+
+
Arnis Druka
+
+Genetics Programme
+
+Scottish Crop Research Institute
+
+Invergowrie, Dundee DD2 5DA
+
+Angus, Scotland, United Kingdom
+
+Tel +44 01382 562731
+Fax +44 01382 568587
+adruka@scri.sari.ac.uk
+
+
+
References:
+
+
+
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64.
+ Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics,
+
+
+Jul;6(3):202-11.
+
+
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
+
+
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
+
+
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
+
+
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
+
+
+
+
+
+
+
About this text file:
+
+
+This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
Barley1 Embryo0 gcRMA SCRI (Apr 06) - integrated probe set value for each gene has been calculated using RMA algorithm (Irizarry et al 2003). RMA ignores MM probe signals. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
+
+
Summary:
+
+
+
The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip.
+
+
+
About the lines used to generate this set of data:
+
+
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
+
+
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
+1)
+pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
+2)
+'minimapper' subset - MINI;
+3) lines that have expression data removed - ERROR:
+
+
+
+
Order #
+
Line ID
+
Permanent Oregon ID
+
Cross direction
+
CEL file names
+
Mini-mapper set
+
Error check
+
+
+
embryo data-set
+
leaf data-set
+
embryo data-set
+
leaf data-set
+
+
+
1
+
SM001
+
2907001
+
Steptoe/Morex(BxF)
+
AD_SCRI_82.CEL
+
+
+
OK
+
+
+
+
2
+
SM002
+
2907002
+
Steptoe/Morex(BxF)
+
AD_SCRI_1.CEL
+
+
+
OK
+
+
+
+
3
+
SM003
+
2907003
+
Morex/Steptoe(CxF)
+
AD_SCRI_19.CEL
+
+
+
OK
+
+
+
+
4
+
SM004
+
2907004
+
Morex/Steptoe(CxF)
+
AD_SCRI_3.CEL
+
0521-1_SetA1.CEL
+
SMmini
+
OK
+
OK
+
+
+
5
+
SM005
+
2907005
+
Steptoe/Morex(BxH)
+
AD_SCRI_88.CEL
+
+
+
OK
+
+
+
+
6
+
SM006
+
2907006
+
Morex/Steptoe(CxF)
+
AD_SCRI_48.CEL
+
+
+
OK
+
+
+
+
7
+
SM007
+
2907007
+
Steptoe/Morex(BxH)
+
AD_SCRI_35.CEL
+
0521-2_SetA2.CEL
+
SMmini
+
OK
+
OK
+
+
+
8
+
SM009
+
2907009
+
Steptoe/Morex(BxF)
+
AD_SCRI_2.CEL
+
+
+
OK
+
+
+
+
9
+
SM010
+
2907010
+
Morex/Steptoe(IxE)
+
AD_SCRI_42.CEL
+
+
+
OK
+
+
+
+
10
+
SM011
+
2907011
+
Steptoe/Morex(QxG)
+
AD_SCRI_10.CEL
+
+
+
OK
+
+
+
+
11
+
SM012
+
2907012
+
Morex/Steptoe(CxF)
+
AD_SCRI_45.CEL
+
0521-3_SetA3.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
12
+
SM013
+
2907013
+
Morex/Steptoe(IxE)
+
AD_SCRI_78.CEL
+
0521-4_SetA4.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
13
+
SM014
+
2907014
+
Steptoe/Morex(BxH)
+
AD_SCRI_18.CEL
+
+
+
OK
+
+
+
+
14
+
SM015
+
2907015
+
Steptoe/Morex(BxH)
+
AD_SCRI_5.CEL
+
+
+
OK
+
+
+
+
15
+
SM016
+
2907016
+
Steptoe/Morex(BxH)
+
AD_SCRI_21.CEL
+
+
+
OK
+
+
+
+
16
+
SM020
+
2907020
+
Steptoe/Morex(OxJ)
+
AD_SCRI_77.CEL
+
+
+
OK
+
+
+
+
17
+
SM021
+
2907021
+
Morex/Steptoe(IxE)
+
AD_SCRI_30.CEL
+
+
+
OK
+
+
+
+
18
+
SM022
+
2907022
+
Morex/Steptoe(IxE)
+
AD_SCRI_31.CEL
+
0521-5_SetA5.CEL
+
SMmini
+
OK
+
OK
+
+
+
19
+
SM023
+
2907023
+
Steptoe/Morex(BxH)
+
AD_SCRI_32.CEL
+
+
+
OK
+
+
+
+
20
+
SM024
+
2907024
+
Morex/Steptoe(IxE)
+
AD_SCRI_33.CEL
+
0521-6_SetA6.CEL
+
SMmini
+
OK
+
OK
+
+
+
21
+
SM025
+
2907025
+
Morex/Steptoe(CxF)
+
AD_SCRI_34.CEL
+
+
+
OK
+
+
+
+
22
+
SM027
+
2907027
+
Steptoe/Morex(OxJ)
+
AD_SCRI_12.CEL
+
0521-7_SetA7.CEL
+
SMmini
+
OK
+
OK
+
+
+
23
+
SM030
+
2907030
+
Morex/Steptoe(IxE)
+
AD_SCRI_79.CEL
+
+
+
OK
+
+
+
+
24
+
SM031
+
2907031
+
Steptoe/Morex(OxJ)
+
AD_SCRI_16.CEL
+
+
+
OK
+
+
+
+
25
+
SM032
+
2907032
+
Morex/Steptoe(IxE)
+
AD_SCRI_13.CEL
+
+
+
OK
+
+
+
+
26
+
SM035
+
2907035
+
Morex/Steptoe(CxF)
+
AD_SCRI_15.CEL
+
+
+
ERROR
+
+
+
+
27
+
SM039
+
2907039
+
Morex/Steptoe(CxF)
+
AD_SCRI_41.CEL
+
+
+
OK
+
+
+
+
28
+
SM040
+
2907040
+
Steptoe/Morex(BxH)
+
AD_SCRI_83.CEL
+
+
+
OK
+
+
+
+
29
+
SM041
+
2907041
+
Steptoe/Morex(OxJ)
+
AD_SCRI_11_redo.CEL
+
0521-8_SetA8.CEL
+
SMmini
+
OK
+
OK
+
+
+
30
+
SM042
+
2907042
+
Morex/Steptoe(CxF)
+
AD_SCRI_57.CEL
+
+
+
OK
+
+
+
+
31
+
SM043
+
2907043
+
Morex/Steptoe(JxE)
+
AD_SCRI_49.CEL
+
0521-9_SetA9.CEL
+
SMmini
+
OK
+
OK
+
+
+
32
+
SM044
+
2907044
+
Steptoe/Morex(OxJ)
+
AD_SCRI_50.CEL
+
0521-10_SetA10.CEL
+
SMmini
+
OK
+
OK
+
+
+
33
+
SM045
+
2907045
+
Steptoe/Morex(BxH)
+
AD_SCRI_51.CEL
+
+
+
OK
+
+
+
+
34
+
SM046
+
2907046
+
Steptoe/Morex(OxJ)
+
AD_SCRI_52.CEL
+
0521-11_SetA11.CEL
+
SMmini
+
OK
+
OK
+
+
+
35
+
SM048
+
2907048
+
Steptoe/Morex(BxF)
+
AD_SCRI_53.CEL
+
+
+
ERROR
+
+
+
+
36
+
SM050
+
2907050
+
Morex/Steptoe(IxE)
+
AD_SCRI_46.CEL
+
+
+
OK
+
+
+
+
37
+
SM054
+
2907054
+
Morex/Steptoe(CxF)
+
AD_SCRI_60.CEL
+
+
+
OK
+
+
+
+
38
+
SM055
+
2907055
+
Steptoe/Morex(OxJ)
+
AD_SCRI_55.CEL
+
+
+
OK
+
+
+
+
39
+
SM056
+
2907056
+
Steptoe/Morex(BxH)
+
AD_SCRI_23.CEL
+
+
+
OK
+
+
+
+
40
+
SM057
+
2907057
+
Morex/Steptoe(CxF)
+
AD_SCRI_24.CEL
+
+
+
OK
+
+
+
+
41
+
SM058
+
2907058
+
Steptoe/Morex(BxF)
+
AD_SCRI_22.CEL
+
+
+
OK
+
+
+
+
42
+
SM059
+
2907059
+
Steptoe/Morex(BxH)
+
AD_SCRI_27.CEL
+
+
+
OK
+
+
+
+
43
+
SM061
+
2907061
+
Morex/Steptoe(LxF)
+
AD_SCRI_81.CEL
+
0521-12_SetA12.CEL
+
SMmini
+
OK
+
OK
+
+
+
44
+
SM062
+
2907062
+
Morex/Steptoe(CxF)
+
AD_SCRI_44.CEL
+
+
+
OK
+
+
+
+
45
+
SM063
+
2907063
+
Steptoe/Morex(OxJ)
+
AD_SCRI_40.CEL
+
0521-13_SetA13.CEL
+
SMmini
+
OK
+
OK
+
+
+
46
+
SM064
+
2907064
+
Morex/Steptoe(CxF)
+
AD_SCRI_87_redo.CEL
+
+
+
OK
+
+
+
+
47
+
SM065
+
2907065
+
Morex/Steptoe(CxF)
+
AD_SCRI_54.CEL
+
+
+
OK
+
+
+
+
48
+
SM067
+
2907067
+
Steptoe/Morex(OxJ)
+
AD_SCRI_73.CEL
+
+
+
OK
+
+
+
+
49
+
SM068
+
2907068
+
Steptoe/Morex(OxG)
+
AD_SCRI_56.CEL
+
+
+
ERROR
+
+
+
+
50
+
SM069
+
2907069
+
Steptoe/Morex(BxH)
+
AD_SCRI_71.CEL
+
+
+
OK
+
+
+
+
51
+
SM070
+
2907070
+
Steptoe/Morex(BxF)
+
AD_SCRI_64.CEL
+
+
+
OK
+
+
+
+
52
+
SM071
+
2907071
+
Steptoe/Morex(BxH)
+
AD_SCRI_58.CEL
+
+
+
OK
+
+
+
+
53
+
SM072
+
2907072
+
Morex/Steptoe(CxF)
+
AD_SCRI_59.CEL
+
+
+
OK
+
+
+
+
54
+
SM073
+
2907073
+
Steptoe/Morex(BxF)
+
AD_SCRI_74.CEL
+
0521-14_SetA14.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
55
+
SM074
+
2907074
+
Morex/Steptoe(CxF)
+
AD_SCRI_25.CEL
+
0521-15_SetA15.CEL
+
SMmini
+
OK
+
OK
+
+
+
56
+
SM075
+
2907075
+
Steptoe/Morex(QxG)
+
AD_SCRI_120.CEL
+
+
+
OK
+
+
+
+
57
+
SM076
+
2907076
+
Steptoe/Morex(BxF)
+
AD_SCRI_112.CEL
+
+
+
OK
+
+
+
+
58
+
SM077
+
2907077
+
Morex/Steptoe(CxF)
+
AD_SCRI_142.CEL
+
+
+
OK
+
+
+
+
59
+
SM078
+
2907078
+
Steptoe/Morex(BxF)
+
AD_SCRI_86.CEL
+
+
+
OK
+
+
+
+
60
+
SM079
+
2907079
+
Morex/Steptoe(CxF)
+
AD_SCRI_153.CEL
+
0521-16_SetA16.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
61
+
SM080
+
2907080
+
Steptoe/Morex(BxF)
+
AD_SCRI_107.CEL
+
+
+
OK
+
+
+
+
62
+
SM081
+
2907081
+
Morex/Steptoe(CxF)
+
AD_SCRI_105.CEL
+
+
+
OK
+
+
+
+
63
+
SM082
+
2907082
+
Steptoe/Morex(BxF)
+
AD_SCRI_97.CEL
+
+
+
OK
+
+
+
+
64
+
SM083
+
2907083
+
Steptoe/Morex(BxF)
+
AD_SCRI_89.CEL
+
+
+
OK
+
+
+
+
65
+
SM084
+
2907084
+
Morex/Steptoe(CxF)
+
AD_SCRI_155.CEL
+
+
+
OK
+
+
+
+
66
+
SM085
+
2907085
+
Morex/Steptoe(IxE)
+
AD_SCRI_149.CEL
+
0521-17_SetA17.CEL
+
SMmini
+
OK
+
OK
+
+
+
67
+
SM087
+
2907087
+
Steptoe/Morex(OxJ)
+
AD_SCRI_113.CEL
+
+
+
OK
+
+
+
+
68
+
SM088
+
2907088
+
Morex/Steptoe(CxF)
+
AD_SCRI_93.CEL
+
0521-18_SetA18.CEL
+
SMmini
+
OK
+
OK
+
+
+
69
+
SM089
+
2907089
+
Steptoe/Morex(OxJ)
+
AD_SCRI_148.CEL
+
0521-19_SetA19.CEL
+
SMmini
+
OK
+
OK
+
+
+
70
+
SM091
+
2907091
+
Morex/Steptoe(CxF)
+
AD_SCRI_110.CEL
+
+
+
OK
+
+
+
+
71
+
SM092
+
2907092
+
Steptoe/Morex(OxJ)
+
AD_SCRI_7.CEL
+
+
+
OK
+
+
+
+
72
+
SM093
+
2907093
+
Steptoe/Morex(BxF)
+
AD_SCRI_122.CEL
+
+
+
OK
+
+
+
+
73
+
SM094
+
2907094
+
Morex/Steptoe(CxF)
+
AD_SCRI_150.CEL
+
+
+
OK
+
+
+
+
74
+
SM097
+
2907097
+
Morex/Steptoe(CxF)
+
AD_SCRI_158.CEL
+
+
+
OK
+
+
+
+
75
+
SM098
+
2907098
+
Morex/Steptoe(CxF)
+
AD_SCRI_121.CEL
+
+
+
OK
+
+
+
+
76
+
SM099
+
2907099
+
Steptoe/Morex(QxG)
+
AD_SCRI_137.CEL
+
+
+
OK
+
+
+
+
77
+
SM103
+
2907103
+
Morex/Steptoe(IxE)
+
AD_SCRI_156.CEL
+
+
+
OK
+
+
+
+
78
+
SM104
+
2907104
+
Steptoe/Morex(BxH)
+
AD_SCRI_70.CEL
+
+
+
ERROR
+
+
+
+
79
+
SM105
+
2907105
+
Morex/Steptoe(IxE)
+
AD_SCRI_69.CEL
+
+
+
OK
+
+
+
+
80
+
SM110
+
2907110
+
Morex/Steptoe(CxF)
+
AD_SCRI_75.CEL
+
+
+
ERROR
+
+
+
+
81
+
SM112
+
2907112
+
Steptoe/Morex(BxF)
+
AD_SCRI_84.CEL
+
+
+
OK
+
+
+
+
82
+
SM116
+
2907116
+
Morex/Steptoe(CxF)
+
AD_SCRI_117.CEL
+
0521-20_SetA20.CEL
+
SMmini
+
OK
+
OK
+
+
+
83
+
SM120
+
2907120
+
Steptoe/Morex(OxJ)
+
AD_SCRI_138.CEL
+
+
+
OK
+
+
+
+
84
+
SM124
+
2907124
+
Steptoe/Morex(BxF)
+
AD_SCRI_146.CEL
+
+
+
OK
+
+
+
+
85
+
SM125
+
2907125
+
Morex/Steptoe(IxE)
+
AD_SCRI_43.CEL
+
+
+
OK
+
+
+
+
86
+
SM126
+
2907126
+
Steptoe/Morex(OxJ)
+
AD_SCRI_144_redo.CEL
+
+
+
OK
+
+
+
+
87
+
SM127
+
2907127
+
Steptoe/Morex(BxH)
+
AD_SCRI_129.CEL
+
+
+
OK
+
+
+
+
88
+
SM129
+
2907129
+
Steptoe/Morex(OxJ)
+
AD_SCRI_132.CEL
+
+
+
OK
+
+
+
+
89
+
SM130
+
2907130
+
Morex/Steptoe(CxF)
+
AD_SCRI_101.CEL
+
0521-21_SetA21.CEL
+
SMmini
+
OK
+
OK
+
+
+
90
+
SM131
+
2907131
+
Steptoe/Morex(OxJ)
+
AD_SCRI_102.CEL
+
+
+
OK
+
+
+
+
91
+
SM132
+
2907132
+
Steptoe/Morex(QxG)
+
AD_SCRI_4_redo.CEL
+
+
+
OK
+
+
+
+
92
+
SM133
+
2907133
+
Morex/Steptoe(CxF)
+
AD_SCRI_157.CEL
+
+
+
OK
+
+
+
+
93
+
SM134
+
2907134
+
Morex/Steptoe(IxE)
+
AD_SCRI_159.CEL
+
+
+
OK
+
+
+
+
94
+
SM135
+
2907135
+
Steptoe/Morex(BxF)
+
AD_SCRI_72.CEL
+
0521-22_SetA22.CEL
+
SMmini
+
OK
+
OK
+
+
+
95
+
SM136
+
2907136
+
Steptoe/Morex(QxG)
+
AD_SCRI_123.CEL
+
0521-23_SetA23.CEL
+
SMmini
+
OK
+
OK
+
+
+
96
+
SM137
+
2907137
+
Steptoe/Morex(BxH)
+
AD_SCRI_39.CEL
+
+
+
OK
+
+
+
+
97
+
SM139
+
2907139
+
Morex/Steptoe(CxF)
+
AD_SCRI_133.CEL
+
+
+
OK
+
+
+
+
98
+
SM140
+
2907140
+
Morex/Steptoe(CxF)
+
AD_SCRI_134.CEL
+
0521-24_SetA24.CEL
+
SMmini
+
OK
+
OK
+
+
+
99
+
SM141
+
2907141
+
Steptoe/Morex(BxH)
+
AD_SCRI_136.CEL
+
0521-25_SetA25.CEL
+
SMmini
+
OK
+
OK
+
+
+
100
+
SM142
+
2907142
+
Morex/Steptoe(IxE)
+
AD_SCRI_6.CEL
+
+
+
OK
+
+
+
+
101
+
SM143
+
2907143
+
Steptoe/Morex(BxH)
+
AD_SCRI_145.CEL
+
+
+
OK
+
+
+
+
102
+
SM144
+
2907144
+
Steptoe/Morex(BxF)
+
AD_SCRI_103.CEL
+
+
+
OK
+
+
+
+
103
+
SM145
+
2907145
+
Steptoe/Morex(QxG)
+
AD_SCRI_108.CEL
+
+
+
OK
+
+
+
+
104
+
SM146
+
2907146
+
Morex/Steptoe(BxF)
+
AD_SCRI_91.CEL
+
0521-26_SetA26.CEL
+
SMmini
+
OK
+
OK
+
+
+
105
+
SM147
+
2907147
+
Steptoe/Morex(OxJ)
+
AD_SCRI_139.CEL
+
+
+
OK
+
+
+
+
106
+
SM149
+
2907149
+
Steptoe/Morex(BxF)
+
AD_SCRI_131.CEL
+
+
+
ERROR
+
+
+
+
107
+
SM150
+
2907150
+
Morex/Steptoe(CxF)
+
AD_SCRI_37.CEL
+
+
+
OK
+
+
+
+
108
+
SM151
+
2907151
+
Morex/Steptoe(IxE)
+
AD_SCRI_28.CEL
+
+
+
OK
+
+
+
+
109
+
SM152
+
2907152
+
Steptoe/Morex(BxH)
+
AD_SCRI_9_redo.CEL
+
0521-27_SetA27.CEL
+
SMmini
+
OK
+
OK
+
+
+
110
+
SM153
+
2907153
+
Steptoe/Morex(BxH)
+
AD_SCRI_135.CEL
+
+
+
OK
+
+
+
+
111
+
SM154
+
2907154
+
Steptoe/Morex(BxH)
+
AD_SCRI_114.CEL
+
+
+
OK
+
+
+
+
112
+
SM155
+
2907155
+
Steptoe/Morex(BxH)
+
AD_SCRI_119.CEL
+
0521-28_SetA28.CEL
+
SMmini
+
OK
+
OK
+
+
+
113
+
SM156
+
2907156
+
Steptoe/Morex(BxH)
+
AD_SCRI_140.CEL
+
+
+
OK
+
+
+
+
114
+
SM157
+
2907157
+
Morex/Steptoe(CxF)
+
AD_SCRI_106_redo.CEL
+
+
+
OK
+
+
+
+
115
+
SM158
+
2907158
+
Morex/Steptoe(CxF)
+
AD_SCRI_65.CEL
+
+
+
OK
+
+
+
+
116
+
SM159
+
2907159
+
Morex/Steptoe(IxE)
+
AD_SCRI_168.CEL
+
+
+
OK
+
+
+
+
117
+
SM160
+
2907160
+
Steptoe/Morex(OxJ)
+
AD_SCRI_47.CEL
+
0521-29_SetA29.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
118
+
SM161
+
2907161
+
Steptoe/Morex(BxH)
+
AD_SCRI_76.CEL
+
+
+
ERROR
+
+
+
+
119
+
SM162
+
2907162
+
Morex/Steptoe(CxF)
+
AD_SCRI_147.CEL
+
+
+
OK
+
+
+
+
120
+
SM164
+
2907164
+
Steptoe/Morex(OxJ)
+
AD_SCRI_128.CEL
+
+
+
OK
+
+
+
+
121
+
SM165
+
2907165
+
Steptoe/Morex(BxH)
+
AD_SCRI_143.CEL
+
+
+
OK
+
OK
+
+
+
122
+
SM166
+
2907166
+
Morex/Steptoe(CxF)
+
AD_SCRI_115.CEL
+
+
+
OK
+
+
+
+
123
+
SM167
+
2907167
+
Steptoe/Morex(BxH)
+
AD_SCRI_127.CEL
+
0521-30_SetA30.CEL
+
SMmini
+
OK
+
OK
+
+
+
124
+
SM168
+
2907168
+
Steptoe/Morex(BxH)
+
AD_SCRI_130.CEL
+
+
+
OK
+
+
+
+
125
+
SM169
+
2907169
+
Morex/Steptoe(CxF)
+
AD_SCRI_118.CEL
+
0521-31_SetA31.CEL
+
SMmini
+
OK
+
OK
+
+
+
126
+
SM170
+
2907170
+
Steptoe/Morex(BxF)
+
AD_SCRI_151.CEL
+
+
+
OK
+
+
+
+
127
+
SM171
+
2907171
+
Steptoe/Morex(BxF)
+
AD_SCRI_165.CEL
+
+
+
ERROR
+
+
+
+
128
+
SM172
+
2907172
+
Steptoe/Morex(OxJ)
+
AD_SCRI_152.CEL
+
+
+
ERROR
+
+
+
+
129
+
SM173
+
2907173
+
Steptoe/Morex(OxJ)
+
AD_SCRI_104.CEL
+
0521-32_SetA32.CEL
+
SMmini
+
OK
+
OK
+
+
+
130
+
SM174
+
2907174
+
Steptoe/Morex(BxH)
+
AD_SCRI_154.CEL
+
+
+
OK
+
+
+
+
131
+
SM176
+
2907176
+
Morex/Steptoe(CxF)
+
AD_SCRI_141.CEL
+
+
+
OK
+
+
+
+
132
+
SM177
+
2907177
+
Morex/Steptoe(CxF)
+
AD_SCRI_111.CEL
+
0521-33_SetA33.CEL
+
SMmini
+
OK
+
OK
+
+
+
133
+
SM179
+
2907179
+
Morex/Steptoe(CxF)
+
AD_SCRI_166.CEL
+
+
+
OK
+
+
+
+
134
+
SM180
+
2907180
+
Morex/Steptoe(IxE)
+
AD_SCRI_161.CEL
+
+
+
OK
+
+
+
+
135
+
SM181
+
2907181
+
Morex/Steptoe(IxE)
+
AD_SCRI_162.CEL
+
+
+
OK
+
+
+
+
136
+
SM182
+
2907182
+
Morex/Steptoe(CxF)
+
AD_SCRI_163.CEL
+
+
+
OK
+
+
+
+
137
+
SM183
+
2907183
+
Morex/Steptoe(CxF)
+
AD_SCRI_164.CEL
+
+
+
OK
+
+
+
+
138
+
SM184
+
2907184
+
Morex/Steptoe(IxE)
+
AD_SCRI_160.CEL
+
0521-34_SetA34.CEL
+
SMmini
+
OK
+
OK
+
+
+
139
+
SM185
+
2907185
+
Morex/Steptoe(IxE)
+
AD_SCRI_167.CEL
+
+
+
OK
+
+
+
+
140
+
SM186
+
2907186
+
Morex/Steptoe(IxE)
+
AD_SCRI_62.CEL
+
+
+
OK
+
+
+
+
141
+
SM187
+
2907187
+
Morex/Steptoe(IxE)
+
AD_SCRI_61.CEL
+
+
+
OK
+
+
+
+
142
+
SM188
+
2907188
+
Morex/Steptoe(CxF)
+
AD_SCRI_63.CEL
+
+
+
OK
+
+
+
+
143
+
SM189
+
2907189
+
Steptoe/Morex(QxG)
+
AD_SCRI_80.CEL
+
+
+
OK
+
+
+
+
144
+
SM193
+
2907193
+
Morex/Steptoe(IxE)
+
AD_SCRI_36.CEL
+
+
+
OK
+
+
+
+
145
+
SM194
+
2907194
+
Steptoe/Morex(OxJ)
+
AD_SCRI_29.CEL
+
+
+
OK
+
+
+
+
146
+
SM196
+
2907196
+
Steptoe/Morex(BxF)
+
AD_SCRI_26.CEL
+
+
+
OK
+
+
+
+
147
+
SM197
+
2907197
+
Steptoe/Morex(BxF)
+
AD_SCRI_85.CEL
+
+
+
OK
+
+
+
+
148
+
SM198
+
2907198
+
Morex/Steptoe(IxE)
+
AD_SCRI_8.CEL
+
+
+
OK
+
+
+
+
149
+
SM199
+
2907199
+
Steptoe/Morex(BxF)
+
AD_SCRI_20.CEL
+
+
+
OK
+
+
+
+
150
+
SM200
+
2907200
+
Morex/Steptoe(IxE)
+
AD_SCRI_38.CEL
+
0521-35_SetA35.CEL
+
SMmini
+
OK
+
OK
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_17.CEL
+
0521-36_SetA36.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_66.CEL
+
0521-37_SetA37.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_68.CEL
+
0521-38_SetA38.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_116.CEL
+
0521-39_SetA39.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_14.CEL
+
0521-40_SetA40.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_67.CEL
+
0521-41_SetA41.CEL
+
+
+
+
+
+
+
+
+
About tissues used to generate this set of data:
+
+
+
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
+
+
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
+
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
+
+
+
+
+
+
RNA Sample Processing:
+
Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
+
+☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
+☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
+☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
+☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
+☐ While centrifuging, label new set of 15 ml tubes
+☐ Transfer supernatant to 15 ml centrifuge tube
+☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
+seconds, and incubate at room temperature for 5 minutes.
+☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
+☐ While centrifuging, label new 15 ml tubes
+☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
+☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
+☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
+☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
+4000 rpm for 15 minutes @ 4oC.
+☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
+☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
+☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
+few times.
+☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
+☐ Set water bath to 37oC.
+☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
+☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
+☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
+☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
+☐ Label 15 ml tubes from the kit and place midi columns in them
+☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
+☐ Discard the flow-through.
+☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
+incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
+☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
+gently, incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
+☐ Centrifuge again for another 5 min.
+☐ Label new 15 ml tubes from the kit.
+☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
+RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ To the same tube add again 250 ul H2O, incubate for 1 min.
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ Label two sets of 1.5 ml Eppendorf tubes.
+☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
+
+
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
+
+
Replication and Sample Balance:
+
3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
+
Experimental Design and Batch Structure:
+
+
+
+
+
+
Downloading complete data set:
+
+
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
+E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
+
+
+
+
About the array platform:
+
+
+
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
+
+
The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
+
+
+
+
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
+Barley1 Leaf MAS 5.0 SCRI (Dec 06)
+
+
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
+
+
+
Values below 0.01 were set to 0.01.
+
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
+
Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
+
+
+
+
+
+
+
+
Data source acknowledgment:
+
+
+
Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant
+
+
+SCR/910/04
+
+'The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
+
+
+
Contact address:
+
+
Arnis Druka
+
+Genetics Programme
+
+Scottish Crop Research Institute
+
+Invergowrie, Dundee DD2 5DA
+
+Angus, Scotland, United Kingdom
+
+Tel +44 01382 562731
+Fax +44 01382 568587
+adruka@scri.sari.ac.uk
+
+
+
References:
+
+
+
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64.
+ Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics,
+
+
+Jul;6(3):202-11.
+
+
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
+
+
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
+
+
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
+
+
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
+
+
+
+
+
+
+
About this text file:
+
+
+This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
Genetics of mRNA abundance in barley
+ Affymetrix RMA data set from SCRI, December 2006
+
+
+
+
+
Summary:
+
+
+
PRELIMINARY TEXT: The December 2006 SCRI barley data set was generated to provide estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip.
+
+
ARNIS: Please revise and update this text. I copied the April 2006 data and have NOT made any modifications below.
+
+
+
+
About the lines used to generate this set of data:
+
+
+
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
+
+
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The following are the IDs of the 35 line subset:
+
Line SM073 has been removed from the analysis of the leaf tissue because it appeared to be a duplicate of SM074, but the data are available from the ArrayExpress.
+
+
The following classical phenotypes have also been deposited in GeneNetwork in the Phenotype file. Full descriptions of the phenotyping procedures are available from Hayes et al. (1993):
+
+
+
Grain yield (MT/ha)
+
Lodging (%)
+
Height (cm)
+
Heading date (days after January 1)
+
Grain protein (%)
+
Alpha amylase (20 Deg units)
+
Diastatic power (Deg)
+
Malt extract (%)
+
+
+
Agronomic and malting quality traits were measured in 16 and 9 environments, respectively. The phenotype data files are coded for each environment as follows:
+Environment #
+
+
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
+
+
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
+
+
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
+
+
+
+
+
RNA Sample Processing:
+
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
+
+
Replication and Sample Balance:
+
+
Experimental Design and Batch Structure:
+
+
+
+
+
+
Downloading all data:
+
+
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
+E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips). Line SM073 was not used in this GeneNetwork data set because it is suspected replicate of SM074.
+
+
+
+
+
About the array platform:
+
+
+
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
+
+
+
+
+
About data processing:
+
+
+
The CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
+
+
Values below 0.01 were set to 0.01.
+
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
+
Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
+
+
+
+
+
+
Data source acknowledgment:
+
+
+
Plant maintenance, tissue collection, RNA isolation, and data preparation for submission to GeneNetwork was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant to Prof. Michael Kearsey (University of Birmingham, UK) and Dr. Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to Arrayexpress.
+
+
+
Contact address:
+
+ Arnis Druka
+ Genetics Programme
+ Scottish Crop Research Institute
+ Invergowrie, Dundee DD2 5DA
+ Angus, Scotland, United Kingdom
+ Tel +44 01382 562731
+ adruka@scri.sari.ac.uk
+
+
+
References:
+
+
+
Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics, in press.
+
+
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
+
+
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
+
+
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
+
+
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
+
+
+
+
+
+
+
About this text file:
+
+This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006.
+
Availability of this data and information does not constitute scientific publication. We request that information derived from it not be published prior to our publication without permission (see below) or 12 months from the time of display whichever is the sooner.
+
+Our policy is to release data in a timely and prompt manner to aid the progress of research in plant-pathogen interactions. However, it is not intended to allow others to preempt our scientific publications by rushing to publication in advance of our own efforts.
+
+Leaf mRNA data was generated by Roger Wise and colleagues. Please reference the key publications below that describes these data and the experimental design in more detail:
+
+
Moscou MJ, Lauter N, Steffenson B, Wise RP (2011) Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genet 7:e1002208
+PDF
+
+
Data were entered into GeneNetwork by Roger Wise, Rob Williams, and colleagues. All MIAME-compliant GeneChip profiling data are available as accession BB64 at the PLEXdb expression resource for plants and plant pathogens (www.plexdb.org), accession GSE20416 at NCBI-GEO, as well as accessions GN235, GN236, GN237, GN238 at GeneNetwork (www.genenetwork.org).
+
+
+Abstract
+
+Stem rust (Puccinia graminis f. sp. tritici; Pgt) is a devastating fungal disease of wheat and barley. Pgt race TTKSK (isolate Ug99) is a serious threat to these Triticeae grain crops because resistance is rare. In barley, the complex Rpg-TTKSK locus on chromosome 5H is presently the only known source of qualitative resistance to this aggressive Pgt race. Segregation for resistance observed on seedlings of the Q21861 × SM89010 (QSM) doubled-haploid (DH) population was found to be predominantly qualitative, with little of the remaining variance explained by loci other than Rpg-TTKSK. In contrast, analysis of adult QSM DH plants infected by field inoculum of Pgt race TTKSK in Njoro, Kenya, revealed several additional quantitative trait loci that contribute to resistance. To molecularly characterize these loci, Barley1 GeneChips were used to measure the expression of 22,792 genes in the QSM population after inoculation with Pgt race TTKSK or mock-inoculation. Comparison of expression Quantitative Trait Loci (eQTL) between treatments revealed an inoculation-dependent expression polymorphism implicating Actin depolymerizing factor3 (within the Rpg-TTKSK locus) as a candidate susceptibility gene. In parallel, we identified a chromosome 2H trans-eQTL hotspot that co-segregates with an enhancer of Rpg-TTKSK-mediated, adult plant resistance discovered through the Njoro field trials. Our genome-wide eQTL studies demonstrate that transcript accumulation of 25% of barley genes is altered following challenge by Pgt race TTKSK, but that few of these genes are regulated by the qualitative Rpg-TTKSK on chromosome 5H. It is instead the chromosome 2H trans-eQTL hotspot that orchestrates the largest inoculation-specific responses, where enhanced resistance is associated with transcriptional suppression of hundreds of genes scattered throughout the genome. Hence, the present study associates the early suppression of genes expressed in this host–pathogen interaction with enhancement of R-gene mediated resistance.
+
+
+
+
Corresponding data on Q/SM resistance to UG99 infection has been generated by Brian Steffenson. The key publication on phenotyping is (not yet entered into GeneNetwork)
+
+
Steffenson BJ, Jin Y, Brueggeman RS, Kleinhofs A, Sun Y (2009) Resistance to stem rust race TTKSK maps to the rpg4/Rpg5 complex of chromosome 5H of barley. Phytopathology 99:1135-41
+
+
+
Availability of this data and information does not constitute scientific publication. We request that information derived from it not be published prior to our publication without permission (see below) or 12 months from the time of display whichever is the sooner.
+
+Our policy is to release data in a timely and prompt manner to aid the progress of research in plant-pathogen interactions. However, it is not intended to allow others to preempt our scientific publications by rushing to publication in advance of our own efforts.
+
Availability of this data and information does not constitute scientific publication. We request that information derived from it not be published prior to our publication without permission (see below) or 12 months from the time of display whichever is the sooner.
+
+Our policy is to release data in a timely and prompt manner to aid the progress of research in plant-pathogen interactions. However, it is not intended to allow others to preempt our scientific publications by rushing to publication in advance of our own efforts.
+
Barley1 Leaf MAS 5.0 SCRI (Dec 06) - integrated probe set value for each gene has been calculated using MAS 5.0 algorithm which uses pixel values from both, PM and MM probes. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
+
+
Summary:
+
+
+
The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip (GEO GPL1340).
+
+
+
About the lines used to generate this set of data:
+
+
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
+
+
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
+1)
+pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
+2)
+'minimapper' subset - MINI;
+3) lines that have expression data removed - ERROR:
+
+
+
+
Order #
+
Line ID
+
Permanent Oregon ID
+
Cross direction
+
CEL file names
+
Mini-mapper set
+
Error check
+
+
+
embryo data-set
+
leaf data-set
+
embryo data-set
+
leaf data-set
+
+
+
1
+
SM001
+
2907001
+
Steptoe/Morex(BxF)
+
AD_SCRI_82.CEL
+
+
+
OK
+
+
+
+
2
+
SM002
+
2907002
+
Steptoe/Morex(BxF)
+
AD_SCRI_1.CEL
+
+
+
OK
+
+
+
+
3
+
SM003
+
2907003
+
Morex/Steptoe(CxF)
+
AD_SCRI_19.CEL
+
+
+
OK
+
+
+
+
4
+
SM004
+
2907004
+
Morex/Steptoe(CxF)
+
AD_SCRI_3.CEL
+
0521-1_SetA1.CEL
+
SMmini
+
OK
+
OK
+
+
+
5
+
SM005
+
2907005
+
Steptoe/Morex(BxH)
+
AD_SCRI_88.CEL
+
+
+
OK
+
+
+
+
6
+
SM006
+
2907006
+
Morex/Steptoe(CxF)
+
AD_SCRI_48.CEL
+
+
+
OK
+
+
+
+
7
+
SM007
+
2907007
+
Steptoe/Morex(BxH)
+
AD_SCRI_35.CEL
+
0521-2_SetA2.CEL
+
SMmini
+
OK
+
OK
+
+
+
8
+
SM009
+
2907009
+
Steptoe/Morex(BxF)
+
AD_SCRI_2.CEL
+
+
+
OK
+
+
+
+
9
+
SM010
+
2907010
+
Morex/Steptoe(IxE)
+
AD_SCRI_42.CEL
+
+
+
OK
+
+
+
+
10
+
SM011
+
2907011
+
Steptoe/Morex(QxG)
+
AD_SCRI_10.CEL
+
+
+
OK
+
+
+
+
11
+
SM012
+
2907012
+
Morex/Steptoe(CxF)
+
AD_SCRI_45.CEL
+
0521-3_SetA3.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
12
+
SM013
+
2907013
+
Morex/Steptoe(IxE)
+
AD_SCRI_78.CEL
+
0521-4_SetA4.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
13
+
SM014
+
2907014
+
Steptoe/Morex(BxH)
+
AD_SCRI_18.CEL
+
+
+
OK
+
+
+
+
14
+
SM015
+
2907015
+
Steptoe/Morex(BxH)
+
AD_SCRI_5.CEL
+
+
+
OK
+
+
+
+
15
+
SM016
+
2907016
+
Steptoe/Morex(BxH)
+
AD_SCRI_21.CEL
+
+
+
OK
+
+
+
+
16
+
SM020
+
2907020
+
Steptoe/Morex(OxJ)
+
AD_SCRI_77.CEL
+
+
+
OK
+
+
+
+
17
+
SM021
+
2907021
+
Morex/Steptoe(IxE)
+
AD_SCRI_30.CEL
+
+
+
OK
+
+
+
+
18
+
SM022
+
2907022
+
Morex/Steptoe(IxE)
+
AD_SCRI_31.CEL
+
0521-5_SetA5.CEL
+
SMmini
+
OK
+
OK
+
+
+
19
+
SM023
+
2907023
+
Steptoe/Morex(BxH)
+
AD_SCRI_32.CEL
+
+
+
OK
+
+
+
+
20
+
SM024
+
2907024
+
Morex/Steptoe(IxE)
+
AD_SCRI_33.CEL
+
0521-6_SetA6.CEL
+
SMmini
+
OK
+
OK
+
+
+
21
+
SM025
+
2907025
+
Morex/Steptoe(CxF)
+
AD_SCRI_34.CEL
+
+
+
OK
+
+
+
+
22
+
SM027
+
2907027
+
Steptoe/Morex(OxJ)
+
AD_SCRI_12.CEL
+
0521-7_SetA7.CEL
+
SMmini
+
OK
+
OK
+
+
+
23
+
SM030
+
2907030
+
Morex/Steptoe(IxE)
+
AD_SCRI_79.CEL
+
+
+
OK
+
+
+
+
24
+
SM031
+
2907031
+
Steptoe/Morex(OxJ)
+
AD_SCRI_16.CEL
+
+
+
OK
+
+
+
+
25
+
SM032
+
2907032
+
Morex/Steptoe(IxE)
+
AD_SCRI_13.CEL
+
+
+
OK
+
+
+
+
26
+
SM035
+
2907035
+
Morex/Steptoe(CxF)
+
AD_SCRI_15.CEL
+
+
+
ERROR
+
+
+
+
27
+
SM039
+
2907039
+
Morex/Steptoe(CxF)
+
AD_SCRI_41.CEL
+
+
+
OK
+
+
+
+
28
+
SM040
+
2907040
+
Steptoe/Morex(BxH)
+
AD_SCRI_83.CEL
+
+
+
OK
+
+
+
+
29
+
SM041
+
2907041
+
Steptoe/Morex(OxJ)
+
AD_SCRI_11_redo.CEL
+
0521-8_SetA8.CEL
+
SMmini
+
OK
+
OK
+
+
+
30
+
SM042
+
2907042
+
Morex/Steptoe(CxF)
+
AD_SCRI_57.CEL
+
+
+
OK
+
+
+
+
31
+
SM043
+
2907043
+
Morex/Steptoe(JxE)
+
AD_SCRI_49.CEL
+
0521-9_SetA9.CEL
+
SMmini
+
OK
+
OK
+
+
+
32
+
SM044
+
2907044
+
Steptoe/Morex(OxJ)
+
AD_SCRI_50.CEL
+
0521-10_SetA10.CEL
+
SMmini
+
OK
+
OK
+
+
+
33
+
SM045
+
2907045
+
Steptoe/Morex(BxH)
+
AD_SCRI_51.CEL
+
+
+
OK
+
+
+
+
34
+
SM046
+
2907046
+
Steptoe/Morex(OxJ)
+
AD_SCRI_52.CEL
+
0521-11_SetA11.CEL
+
SMmini
+
OK
+
OK
+
+
+
35
+
SM048
+
2907048
+
Steptoe/Morex(BxF)
+
AD_SCRI_53.CEL
+
+
+
ERROR
+
+
+
+
36
+
SM050
+
2907050
+
Morex/Steptoe(IxE)
+
AD_SCRI_46.CEL
+
+
+
OK
+
+
+
+
37
+
SM054
+
2907054
+
Morex/Steptoe(CxF)
+
AD_SCRI_60.CEL
+
+
+
OK
+
+
+
+
38
+
SM055
+
2907055
+
Steptoe/Morex(OxJ)
+
AD_SCRI_55.CEL
+
+
+
OK
+
+
+
+
39
+
SM056
+
2907056
+
Steptoe/Morex(BxH)
+
AD_SCRI_23.CEL
+
+
+
OK
+
+
+
+
40
+
SM057
+
2907057
+
Morex/Steptoe(CxF)
+
AD_SCRI_24.CEL
+
+
+
OK
+
+
+
+
41
+
SM058
+
2907058
+
Steptoe/Morex(BxF)
+
AD_SCRI_22.CEL
+
+
+
OK
+
+
+
+
42
+
SM059
+
2907059
+
Steptoe/Morex(BxH)
+
AD_SCRI_27.CEL
+
+
+
OK
+
+
+
+
43
+
SM061
+
2907061
+
Morex/Steptoe(LxF)
+
AD_SCRI_81.CEL
+
0521-12_SetA12.CEL
+
SMmini
+
OK
+
OK
+
+
+
44
+
SM062
+
2907062
+
Morex/Steptoe(CxF)
+
AD_SCRI_44.CEL
+
+
+
OK
+
+
+
+
45
+
SM063
+
2907063
+
Steptoe/Morex(OxJ)
+
AD_SCRI_40.CEL
+
0521-13_SetA13.CEL
+
SMmini
+
OK
+
OK
+
+
+
46
+
SM064
+
2907064
+
Morex/Steptoe(CxF)
+
AD_SCRI_87_redo.CEL
+
+
+
OK
+
+
+
+
47
+
SM065
+
2907065
+
Morex/Steptoe(CxF)
+
AD_SCRI_54.CEL
+
+
+
OK
+
+
+
+
48
+
SM067
+
2907067
+
Steptoe/Morex(OxJ)
+
AD_SCRI_73.CEL
+
+
+
OK
+
+
+
+
49
+
SM068
+
2907068
+
Steptoe/Morex(OxG)
+
AD_SCRI_56.CEL
+
+
+
ERROR
+
+
+
+
50
+
SM069
+
2907069
+
Steptoe/Morex(BxH)
+
AD_SCRI_71.CEL
+
+
+
OK
+
+
+
+
51
+
SM070
+
2907070
+
Steptoe/Morex(BxF)
+
AD_SCRI_64.CEL
+
+
+
OK
+
+
+
+
52
+
SM071
+
2907071
+
Steptoe/Morex(BxH)
+
AD_SCRI_58.CEL
+
+
+
OK
+
+
+
+
53
+
SM072
+
2907072
+
Morex/Steptoe(CxF)
+
AD_SCRI_59.CEL
+
+
+
OK
+
+
+
+
54
+
SM073
+
2907073
+
Steptoe/Morex(BxF)
+
AD_SCRI_74.CEL
+
0521-14_SetA14.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
55
+
SM074
+
2907074
+
Morex/Steptoe(CxF)
+
AD_SCRI_25.CEL
+
0521-15_SetA15.CEL
+
SMmini
+
OK
+
OK
+
+
+
56
+
SM075
+
2907075
+
Steptoe/Morex(QxG)
+
AD_SCRI_120.CEL
+
+
+
OK
+
+
+
+
57
+
SM076
+
2907076
+
Steptoe/Morex(BxF)
+
AD_SCRI_112.CEL
+
+
+
OK
+
+
+
+
58
+
SM077
+
2907077
+
Morex/Steptoe(CxF)
+
AD_SCRI_142.CEL
+
+
+
OK
+
+
+
+
59
+
SM078
+
2907078
+
Steptoe/Morex(BxF)
+
AD_SCRI_86.CEL
+
+
+
OK
+
+
+
+
60
+
SM079
+
2907079
+
Morex/Steptoe(CxF)
+
AD_SCRI_153.CEL
+
0521-16_SetA16.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
61
+
SM080
+
2907080
+
Steptoe/Morex(BxF)
+
AD_SCRI_107.CEL
+
+
+
OK
+
+
+
+
62
+
SM081
+
2907081
+
Morex/Steptoe(CxF)
+
AD_SCRI_105.CEL
+
+
+
OK
+
+
+
+
63
+
SM082
+
2907082
+
Steptoe/Morex(BxF)
+
AD_SCRI_97.CEL
+
+
+
OK
+
+
+
+
64
+
SM083
+
2907083
+
Steptoe/Morex(BxF)
+
AD_SCRI_89.CEL
+
+
+
OK
+
+
+
+
65
+
SM084
+
2907084
+
Morex/Steptoe(CxF)
+
AD_SCRI_155.CEL
+
+
+
OK
+
+
+
+
66
+
SM085
+
2907085
+
Morex/Steptoe(IxE)
+
AD_SCRI_149.CEL
+
0521-17_SetA17.CEL
+
SMmini
+
OK
+
OK
+
+
+
67
+
SM087
+
2907087
+
Steptoe/Morex(OxJ)
+
AD_SCRI_113.CEL
+
+
+
OK
+
+
+
+
68
+
SM088
+
2907088
+
Morex/Steptoe(CxF)
+
AD_SCRI_93.CEL
+
0521-18_SetA18.CEL
+
SMmini
+
OK
+
OK
+
+
+
69
+
SM089
+
2907089
+
Steptoe/Morex(OxJ)
+
AD_SCRI_148.CEL
+
0521-19_SetA19.CEL
+
SMmini
+
OK
+
OK
+
+
+
70
+
SM091
+
2907091
+
Morex/Steptoe(CxF)
+
AD_SCRI_110.CEL
+
+
+
OK
+
+
+
+
71
+
SM092
+
2907092
+
Steptoe/Morex(OxJ)
+
AD_SCRI_7.CEL
+
+
+
OK
+
+
+
+
72
+
SM093
+
2907093
+
Steptoe/Morex(BxF)
+
AD_SCRI_122.CEL
+
+
+
OK
+
+
+
+
73
+
SM094
+
2907094
+
Morex/Steptoe(CxF)
+
AD_SCRI_150.CEL
+
+
+
OK
+
+
+
+
74
+
SM097
+
2907097
+
Morex/Steptoe(CxF)
+
AD_SCRI_158.CEL
+
+
+
OK
+
+
+
+
75
+
SM098
+
2907098
+
Morex/Steptoe(CxF)
+
AD_SCRI_121.CEL
+
+
+
OK
+
+
+
+
76
+
SM099
+
2907099
+
Steptoe/Morex(QxG)
+
AD_SCRI_137.CEL
+
+
+
OK
+
+
+
+
77
+
SM103
+
2907103
+
Morex/Steptoe(IxE)
+
AD_SCRI_156.CEL
+
+
+
OK
+
+
+
+
78
+
SM104
+
2907104
+
Steptoe/Morex(BxH)
+
AD_SCRI_70.CEL
+
+
+
ERROR
+
+
+
+
79
+
SM105
+
2907105
+
Morex/Steptoe(IxE)
+
AD_SCRI_69.CEL
+
+
+
OK
+
+
+
+
80
+
SM110
+
2907110
+
Morex/Steptoe(CxF)
+
AD_SCRI_75.CEL
+
+
+
ERROR
+
+
+
+
81
+
SM112
+
2907112
+
Steptoe/Morex(BxF)
+
AD_SCRI_84.CEL
+
+
+
OK
+
+
+
+
82
+
SM116
+
2907116
+
Morex/Steptoe(CxF)
+
AD_SCRI_117.CEL
+
0521-20_SetA20.CEL
+
SMmini
+
OK
+
OK
+
+
+
83
+
SM120
+
2907120
+
Steptoe/Morex(OxJ)
+
AD_SCRI_138.CEL
+
+
+
OK
+
+
+
+
84
+
SM124
+
2907124
+
Steptoe/Morex(BxF)
+
AD_SCRI_146.CEL
+
+
+
OK
+
+
+
+
85
+
SM125
+
2907125
+
Morex/Steptoe(IxE)
+
AD_SCRI_43.CEL
+
+
+
OK
+
+
+
+
86
+
SM126
+
2907126
+
Steptoe/Morex(OxJ)
+
AD_SCRI_144_redo.CEL
+
+
+
OK
+
+
+
+
87
+
SM127
+
2907127
+
Steptoe/Morex(BxH)
+
AD_SCRI_129.CEL
+
+
+
OK
+
+
+
+
88
+
SM129
+
2907129
+
Steptoe/Morex(OxJ)
+
AD_SCRI_132.CEL
+
+
+
OK
+
+
+
+
89
+
SM130
+
2907130
+
Morex/Steptoe(CxF)
+
AD_SCRI_101.CEL
+
0521-21_SetA21.CEL
+
SMmini
+
OK
+
OK
+
+
+
90
+
SM131
+
2907131
+
Steptoe/Morex(OxJ)
+
AD_SCRI_102.CEL
+
+
+
OK
+
+
+
+
91
+
SM132
+
2907132
+
Steptoe/Morex(QxG)
+
AD_SCRI_4_redo.CEL
+
+
+
OK
+
+
+
+
92
+
SM133
+
2907133
+
Morex/Steptoe(CxF)
+
AD_SCRI_157.CEL
+
+
+
OK
+
+
+
+
93
+
SM134
+
2907134
+
Morex/Steptoe(IxE)
+
AD_SCRI_159.CEL
+
+
+
OK
+
+
+
+
94
+
SM135
+
2907135
+
Steptoe/Morex(BxF)
+
AD_SCRI_72.CEL
+
0521-22_SetA22.CEL
+
SMmini
+
OK
+
OK
+
+
+
95
+
SM136
+
2907136
+
Steptoe/Morex(QxG)
+
AD_SCRI_123.CEL
+
0521-23_SetA23.CEL
+
SMmini
+
OK
+
OK
+
+
+
96
+
SM137
+
2907137
+
Steptoe/Morex(BxH)
+
AD_SCRI_39.CEL
+
+
+
OK
+
+
+
+
97
+
SM139
+
2907139
+
Morex/Steptoe(CxF)
+
AD_SCRI_133.CEL
+
+
+
OK
+
+
+
+
98
+
SM140
+
2907140
+
Morex/Steptoe(CxF)
+
AD_SCRI_134.CEL
+
0521-24_SetA24.CEL
+
SMmini
+
OK
+
OK
+
+
+
99
+
SM141
+
2907141
+
Steptoe/Morex(BxH)
+
AD_SCRI_136.CEL
+
0521-25_SetA25.CEL
+
SMmini
+
OK
+
OK
+
+
+
100
+
SM142
+
2907142
+
Morex/Steptoe(IxE)
+
AD_SCRI_6.CEL
+
+
+
OK
+
+
+
+
101
+
SM143
+
2907143
+
Steptoe/Morex(BxH)
+
AD_SCRI_145.CEL
+
+
+
OK
+
+
+
+
102
+
SM144
+
2907144
+
Steptoe/Morex(BxF)
+
AD_SCRI_103.CEL
+
+
+
OK
+
+
+
+
103
+
SM145
+
2907145
+
Steptoe/Morex(QxG)
+
AD_SCRI_108.CEL
+
+
+
OK
+
+
+
+
104
+
SM146
+
2907146
+
Morex/Steptoe(BxF)
+
AD_SCRI_91.CEL
+
0521-26_SetA26.CEL
+
SMmini
+
OK
+
OK
+
+
+
105
+
SM147
+
2907147
+
Steptoe/Morex(OxJ)
+
AD_SCRI_139.CEL
+
+
+
OK
+
+
+
+
106
+
SM149
+
2907149
+
Steptoe/Morex(BxF)
+
AD_SCRI_131.CEL
+
+
+
ERROR
+
+
+
+
107
+
SM150
+
2907150
+
Morex/Steptoe(CxF)
+
AD_SCRI_37.CEL
+
+
+
OK
+
+
+
+
108
+
SM151
+
2907151
+
Morex/Steptoe(IxE)
+
AD_SCRI_28.CEL
+
+
+
OK
+
+
+
+
109
+
SM152
+
2907152
+
Steptoe/Morex(BxH)
+
AD_SCRI_9_redo.CEL
+
0521-27_SetA27.CEL
+
SMmini
+
OK
+
OK
+
+
+
110
+
SM153
+
2907153
+
Steptoe/Morex(BxH)
+
AD_SCRI_135.CEL
+
+
+
OK
+
+
+
+
111
+
SM154
+
2907154
+
Steptoe/Morex(BxH)
+
AD_SCRI_114.CEL
+
+
+
OK
+
+
+
+
112
+
SM155
+
2907155
+
Steptoe/Morex(BxH)
+
AD_SCRI_119.CEL
+
0521-28_SetA28.CEL
+
SMmini
+
OK
+
OK
+
+
+
113
+
SM156
+
2907156
+
Steptoe/Morex(BxH)
+
AD_SCRI_140.CEL
+
+
+
OK
+
+
+
+
114
+
SM157
+
2907157
+
Morex/Steptoe(CxF)
+
AD_SCRI_106_redo.CEL
+
+
+
OK
+
+
+
+
115
+
SM158
+
2907158
+
Morex/Steptoe(CxF)
+
AD_SCRI_65.CEL
+
+
+
OK
+
+
+
+
116
+
SM159
+
2907159
+
Morex/Steptoe(IxE)
+
AD_SCRI_168.CEL
+
+
+
OK
+
+
+
+
117
+
SM160
+
2907160
+
Steptoe/Morex(OxJ)
+
AD_SCRI_47.CEL
+
0521-29_SetA29.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
118
+
SM161
+
2907161
+
Steptoe/Morex(BxH)
+
AD_SCRI_76.CEL
+
+
+
ERROR
+
+
+
+
119
+
SM162
+
2907162
+
Morex/Steptoe(CxF)
+
AD_SCRI_147.CEL
+
+
+
OK
+
+
+
+
120
+
SM164
+
2907164
+
Steptoe/Morex(OxJ)
+
AD_SCRI_128.CEL
+
+
+
OK
+
+
+
+
121
+
SM165
+
2907165
+
Steptoe/Morex(BxH)
+
AD_SCRI_143.CEL
+
+
+
OK
+
OK
+
+
+
122
+
SM166
+
2907166
+
Morex/Steptoe(CxF)
+
AD_SCRI_115.CEL
+
+
+
OK
+
+
+
+
123
+
SM167
+
2907167
+
Steptoe/Morex(BxH)
+
AD_SCRI_127.CEL
+
0521-30_SetA30.CEL
+
SMmini
+
OK
+
OK
+
+
+
124
+
SM168
+
2907168
+
Steptoe/Morex(BxH)
+
AD_SCRI_130.CEL
+
+
+
OK
+
+
+
+
125
+
SM169
+
2907169
+
Morex/Steptoe(CxF)
+
AD_SCRI_118.CEL
+
0521-31_SetA31.CEL
+
SMmini
+
OK
+
OK
+
+
+
126
+
SM170
+
2907170
+
Steptoe/Morex(BxF)
+
AD_SCRI_151.CEL
+
+
+
OK
+
+
+
+
127
+
SM171
+
2907171
+
Steptoe/Morex(BxF)
+
AD_SCRI_165.CEL
+
+
+
ERROR
+
+
+
+
128
+
SM172
+
2907172
+
Steptoe/Morex(OxJ)
+
AD_SCRI_152.CEL
+
+
+
ERROR
+
+
+
+
129
+
SM173
+
2907173
+
Steptoe/Morex(OxJ)
+
AD_SCRI_104.CEL
+
0521-32_SetA32.CEL
+
SMmini
+
OK
+
OK
+
+
+
130
+
SM174
+
2907174
+
Steptoe/Morex(BxH)
+
AD_SCRI_154.CEL
+
+
+
OK
+
+
+
+
131
+
SM176
+
2907176
+
Morex/Steptoe(CxF)
+
AD_SCRI_141.CEL
+
+
+
OK
+
+
+
+
132
+
SM177
+
2907177
+
Morex/Steptoe(CxF)
+
AD_SCRI_111.CEL
+
0521-33_SetA33.CEL
+
SMmini
+
OK
+
OK
+
+
+
133
+
SM179
+
2907179
+
Morex/Steptoe(CxF)
+
AD_SCRI_166.CEL
+
+
+
OK
+
+
+
+
134
+
SM180
+
2907180
+
Morex/Steptoe(IxE)
+
AD_SCRI_161.CEL
+
+
+
OK
+
+
+
+
135
+
SM181
+
2907181
+
Morex/Steptoe(IxE)
+
AD_SCRI_162.CEL
+
+
+
OK
+
+
+
+
136
+
SM182
+
2907182
+
Morex/Steptoe(CxF)
+
AD_SCRI_163.CEL
+
+
+
OK
+
+
+
+
137
+
SM183
+
2907183
+
Morex/Steptoe(CxF)
+
AD_SCRI_164.CEL
+
+
+
OK
+
+
+
+
138
+
SM184
+
2907184
+
Morex/Steptoe(IxE)
+
AD_SCRI_160.CEL
+
0521-34_SetA34.CEL
+
SMmini
+
OK
+
OK
+
+
+
139
+
SM185
+
2907185
+
Morex/Steptoe(IxE)
+
AD_SCRI_167.CEL
+
+
+
OK
+
+
+
+
140
+
SM186
+
2907186
+
Morex/Steptoe(IxE)
+
AD_SCRI_62.CEL
+
+
+
OK
+
+
+
+
141
+
SM187
+
2907187
+
Morex/Steptoe(IxE)
+
AD_SCRI_61.CEL
+
+
+
OK
+
+
+
+
142
+
SM188
+
2907188
+
Morex/Steptoe(CxF)
+
AD_SCRI_63.CEL
+
+
+
OK
+
+
+
+
143
+
SM189
+
2907189
+
Steptoe/Morex(QxG)
+
AD_SCRI_80.CEL
+
+
+
OK
+
+
+
+
144
+
SM193
+
2907193
+
Morex/Steptoe(IxE)
+
AD_SCRI_36.CEL
+
+
+
OK
+
+
+
+
145
+
SM194
+
2907194
+
Steptoe/Morex(OxJ)
+
AD_SCRI_29.CEL
+
+
+
OK
+
+
+
+
146
+
SM196
+
2907196
+
Steptoe/Morex(BxF)
+
AD_SCRI_26.CEL
+
+
+
OK
+
+
+
+
147
+
SM197
+
2907197
+
Steptoe/Morex(BxF)
+
AD_SCRI_85.CEL
+
+
+
OK
+
+
+
+
148
+
SM198
+
2907198
+
Morex/Steptoe(IxE)
+
AD_SCRI_8.CEL
+
+
+
OK
+
+
+
+
149
+
SM199
+
2907199
+
Steptoe/Morex(BxF)
+
AD_SCRI_20.CEL
+
+
+
OK
+
+
+
+
150
+
SM200
+
2907200
+
Morex/Steptoe(IxE)
+
AD_SCRI_38.CEL
+
0521-35_SetA35.CEL
+
SMmini
+
OK
+
OK
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_17.CEL
+
0521-36_SetA36.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_66.CEL
+
0521-37_SetA37.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_68.CEL
+
0521-38_SetA38.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_116.CEL
+
0521-39_SetA39.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_14.CEL
+
0521-40_SetA40.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_67.CEL
+
0521-41_SetA41.CEL
+
+
+
+
+
+
+
+
+
About tissues used to generate this set of data:
+
+
+
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
+
+
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
+
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
+
+
+
+
+
+
RNA Sample Processing:
+
Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
+
+☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
+☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
+☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
+☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
+☐ While centrifuging, label new set of 15 ml tubes
+☐ Transfer supernatant to 15 ml centrifuge tube
+☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
+seconds, and incubate at room temperature for 5 minutes.
+☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
+☐ While centrifuging, label new 15 ml tubes
+☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
+☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
+☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
+☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
+4000 rpm for 15 minutes @ 4oC.
+☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
+☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
+☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
+few times.
+☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
+☐ Set water bath to 37oC.
+☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
+☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
+☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
+☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
+☐ Label 15 ml tubes from the kit and place midi columns in them
+☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
+☐ Discard the flow-through.
+☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
+incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
+☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
+gently, incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
+☐ Centrifuge again for another 5 min.
+☐ Label new 15 ml tubes from the kit.
+☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
+RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ To the same tube add again 250 ul H2O, incubate for 1 min.
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ Label two sets of 1.5 ml Eppendorf tubes.
+☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
+
+
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
+
+
Replication and Sample Balance:
+
3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
+
Experimental Design and Batch Structure:
+
+
+
+
+
+
Downloading complete data set:
+
+
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
+E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
+
+
+
+
About the array platform:
+
+
+
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
+
+
The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
+
+
+
+
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
+Barley1 Leaf MAS 5.0 SCRI (Dec 06)
+
+
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
+
+
+
Values below 0.01 were set to 0.01.
+
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
+
Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
+
+
+
+
+
+
+
+
Data source acknowledgment:
+
+
+
Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant
+
+
+SCR/910/04
+
+'The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
+
+
+
Contact address:
+
+
Arnis Druka
+
+Genetics Programme
+
+Scottish Crop Research Institute
+
+Invergowrie, Dundee DD2 5DA
+
+Angus, Scotland, United Kingdom
+
+Tel +44 01382 562731
+Fax +44 01382 568587
+adruka@scri.sari.ac.uk
+
+
+
References:
+
+
+
Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics, Jul;6(3):202-11.
+
+
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
+
+
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
+
+
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
+
+
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
+
+
+
+
+
+
+
About this text file:
+
+
+This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
Barley1 Leaf gcRMA SCRI (Dec 06) - integrated probe set value for each gene has been calculated using RMA algorithm (Irizarry et al 2003). RMA ignores MM probe signals. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
+
+
Summary:
+
+
+
The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip.
+
+
+
About the lines used to generate this set of data:
+
+
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
+
+
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
+1)
+pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
+2)
+'minimapper' subset - MINI;
+3) lines that have expression data removed - ERROR:
+
+
+
+
Order #
+
Line ID
+
Permanent Oregon ID
+
Cross direction
+
CEL file names
+
Mini-mapper set
+
Error check
+
+
+
embryo data-set
+
leaf data-set
+
embryo data-set
+
leaf data-set
+
+
+
1
+
SM001
+
2907001
+
Steptoe/Morex(BxF)
+
AD_SCRI_82.CEL
+
+
+
OK
+
+
+
+
2
+
SM002
+
2907002
+
Steptoe/Morex(BxF)
+
AD_SCRI_1.CEL
+
+
+
OK
+
+
+
+
3
+
SM003
+
2907003
+
Morex/Steptoe(CxF)
+
AD_SCRI_19.CEL
+
+
+
OK
+
+
+
+
4
+
SM004
+
2907004
+
Morex/Steptoe(CxF)
+
AD_SCRI_3.CEL
+
0521-1_SetA1.CEL
+
SMmini
+
OK
+
OK
+
+
+
5
+
SM005
+
2907005
+
Steptoe/Morex(BxH)
+
AD_SCRI_88.CEL
+
+
+
OK
+
+
+
+
6
+
SM006
+
2907006
+
Morex/Steptoe(CxF)
+
AD_SCRI_48.CEL
+
+
+
OK
+
+
+
+
7
+
SM007
+
2907007
+
Steptoe/Morex(BxH)
+
AD_SCRI_35.CEL
+
0521-2_SetA2.CEL
+
SMmini
+
OK
+
OK
+
+
+
8
+
SM009
+
2907009
+
Steptoe/Morex(BxF)
+
AD_SCRI_2.CEL
+
+
+
OK
+
+
+
+
9
+
SM010
+
2907010
+
Morex/Steptoe(IxE)
+
AD_SCRI_42.CEL
+
+
+
OK
+
+
+
+
10
+
SM011
+
2907011
+
Steptoe/Morex(QxG)
+
AD_SCRI_10.CEL
+
+
+
OK
+
+
+
+
11
+
SM012
+
2907012
+
Morex/Steptoe(CxF)
+
AD_SCRI_45.CEL
+
0521-3_SetA3.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
12
+
SM013
+
2907013
+
Morex/Steptoe(IxE)
+
AD_SCRI_78.CEL
+
0521-4_SetA4.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
13
+
SM014
+
2907014
+
Steptoe/Morex(BxH)
+
AD_SCRI_18.CEL
+
+
+
OK
+
+
+
+
14
+
SM015
+
2907015
+
Steptoe/Morex(BxH)
+
AD_SCRI_5.CEL
+
+
+
OK
+
+
+
+
15
+
SM016
+
2907016
+
Steptoe/Morex(BxH)
+
AD_SCRI_21.CEL
+
+
+
OK
+
+
+
+
16
+
SM020
+
2907020
+
Steptoe/Morex(OxJ)
+
AD_SCRI_77.CEL
+
+
+
OK
+
+
+
+
17
+
SM021
+
2907021
+
Morex/Steptoe(IxE)
+
AD_SCRI_30.CEL
+
+
+
OK
+
+
+
+
18
+
SM022
+
2907022
+
Morex/Steptoe(IxE)
+
AD_SCRI_31.CEL
+
0521-5_SetA5.CEL
+
SMmini
+
OK
+
OK
+
+
+
19
+
SM023
+
2907023
+
Steptoe/Morex(BxH)
+
AD_SCRI_32.CEL
+
+
+
OK
+
+
+
+
20
+
SM024
+
2907024
+
Morex/Steptoe(IxE)
+
AD_SCRI_33.CEL
+
0521-6_SetA6.CEL
+
SMmini
+
OK
+
OK
+
+
+
21
+
SM025
+
2907025
+
Morex/Steptoe(CxF)
+
AD_SCRI_34.CEL
+
+
+
OK
+
+
+
+
22
+
SM027
+
2907027
+
Steptoe/Morex(OxJ)
+
AD_SCRI_12.CEL
+
0521-7_SetA7.CEL
+
SMmini
+
OK
+
OK
+
+
+
23
+
SM030
+
2907030
+
Morex/Steptoe(IxE)
+
AD_SCRI_79.CEL
+
+
+
OK
+
+
+
+
24
+
SM031
+
2907031
+
Steptoe/Morex(OxJ)
+
AD_SCRI_16.CEL
+
+
+
OK
+
+
+
+
25
+
SM032
+
2907032
+
Morex/Steptoe(IxE)
+
AD_SCRI_13.CEL
+
+
+
OK
+
+
+
+
26
+
SM035
+
2907035
+
Morex/Steptoe(CxF)
+
AD_SCRI_15.CEL
+
+
+
ERROR
+
+
+
+
27
+
SM039
+
2907039
+
Morex/Steptoe(CxF)
+
AD_SCRI_41.CEL
+
+
+
OK
+
+
+
+
28
+
SM040
+
2907040
+
Steptoe/Morex(BxH)
+
AD_SCRI_83.CEL
+
+
+
OK
+
+
+
+
29
+
SM041
+
2907041
+
Steptoe/Morex(OxJ)
+
AD_SCRI_11_redo.CEL
+
0521-8_SetA8.CEL
+
SMmini
+
OK
+
OK
+
+
+
30
+
SM042
+
2907042
+
Morex/Steptoe(CxF)
+
AD_SCRI_57.CEL
+
+
+
OK
+
+
+
+
31
+
SM043
+
2907043
+
Morex/Steptoe(JxE)
+
AD_SCRI_49.CEL
+
0521-9_SetA9.CEL
+
SMmini
+
OK
+
OK
+
+
+
32
+
SM044
+
2907044
+
Steptoe/Morex(OxJ)
+
AD_SCRI_50.CEL
+
0521-10_SetA10.CEL
+
SMmini
+
OK
+
OK
+
+
+
33
+
SM045
+
2907045
+
Steptoe/Morex(BxH)
+
AD_SCRI_51.CEL
+
+
+
OK
+
+
+
+
34
+
SM046
+
2907046
+
Steptoe/Morex(OxJ)
+
AD_SCRI_52.CEL
+
0521-11_SetA11.CEL
+
SMmini
+
OK
+
OK
+
+
+
35
+
SM048
+
2907048
+
Steptoe/Morex(BxF)
+
AD_SCRI_53.CEL
+
+
+
ERROR
+
+
+
+
36
+
SM050
+
2907050
+
Morex/Steptoe(IxE)
+
AD_SCRI_46.CEL
+
+
+
OK
+
+
+
+
37
+
SM054
+
2907054
+
Morex/Steptoe(CxF)
+
AD_SCRI_60.CEL
+
+
+
OK
+
+
+
+
38
+
SM055
+
2907055
+
Steptoe/Morex(OxJ)
+
AD_SCRI_55.CEL
+
+
+
OK
+
+
+
+
39
+
SM056
+
2907056
+
Steptoe/Morex(BxH)
+
AD_SCRI_23.CEL
+
+
+
OK
+
+
+
+
40
+
SM057
+
2907057
+
Morex/Steptoe(CxF)
+
AD_SCRI_24.CEL
+
+
+
OK
+
+
+
+
41
+
SM058
+
2907058
+
Steptoe/Morex(BxF)
+
AD_SCRI_22.CEL
+
+
+
OK
+
+
+
+
42
+
SM059
+
2907059
+
Steptoe/Morex(BxH)
+
AD_SCRI_27.CEL
+
+
+
OK
+
+
+
+
43
+
SM061
+
2907061
+
Morex/Steptoe(LxF)
+
AD_SCRI_81.CEL
+
0521-12_SetA12.CEL
+
SMmini
+
OK
+
OK
+
+
+
44
+
SM062
+
2907062
+
Morex/Steptoe(CxF)
+
AD_SCRI_44.CEL
+
+
+
OK
+
+
+
+
45
+
SM063
+
2907063
+
Steptoe/Morex(OxJ)
+
AD_SCRI_40.CEL
+
0521-13_SetA13.CEL
+
SMmini
+
OK
+
OK
+
+
+
46
+
SM064
+
2907064
+
Morex/Steptoe(CxF)
+
AD_SCRI_87_redo.CEL
+
+
+
OK
+
+
+
+
47
+
SM065
+
2907065
+
Morex/Steptoe(CxF)
+
AD_SCRI_54.CEL
+
+
+
OK
+
+
+
+
48
+
SM067
+
2907067
+
Steptoe/Morex(OxJ)
+
AD_SCRI_73.CEL
+
+
+
OK
+
+
+
+
49
+
SM068
+
2907068
+
Steptoe/Morex(OxG)
+
AD_SCRI_56.CEL
+
+
+
ERROR
+
+
+
+
50
+
SM069
+
2907069
+
Steptoe/Morex(BxH)
+
AD_SCRI_71.CEL
+
+
+
OK
+
+
+
+
51
+
SM070
+
2907070
+
Steptoe/Morex(BxF)
+
AD_SCRI_64.CEL
+
+
+
OK
+
+
+
+
52
+
SM071
+
2907071
+
Steptoe/Morex(BxH)
+
AD_SCRI_58.CEL
+
+
+
OK
+
+
+
+
53
+
SM072
+
2907072
+
Morex/Steptoe(CxF)
+
AD_SCRI_59.CEL
+
+
+
OK
+
+
+
+
54
+
SM073
+
2907073
+
Steptoe/Morex(BxF)
+
AD_SCRI_74.CEL
+
0521-14_SetA14.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
55
+
SM074
+
2907074
+
Morex/Steptoe(CxF)
+
AD_SCRI_25.CEL
+
0521-15_SetA15.CEL
+
SMmini
+
OK
+
OK
+
+
+
56
+
SM075
+
2907075
+
Steptoe/Morex(QxG)
+
AD_SCRI_120.CEL
+
+
+
OK
+
+
+
+
57
+
SM076
+
2907076
+
Steptoe/Morex(BxF)
+
AD_SCRI_112.CEL
+
+
+
OK
+
+
+
+
58
+
SM077
+
2907077
+
Morex/Steptoe(CxF)
+
AD_SCRI_142.CEL
+
+
+
OK
+
+
+
+
59
+
SM078
+
2907078
+
Steptoe/Morex(BxF)
+
AD_SCRI_86.CEL
+
+
+
OK
+
+
+
+
60
+
SM079
+
2907079
+
Morex/Steptoe(CxF)
+
AD_SCRI_153.CEL
+
0521-16_SetA16.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
61
+
SM080
+
2907080
+
Steptoe/Morex(BxF)
+
AD_SCRI_107.CEL
+
+
+
OK
+
+
+
+
62
+
SM081
+
2907081
+
Morex/Steptoe(CxF)
+
AD_SCRI_105.CEL
+
+
+
OK
+
+
+
+
63
+
SM082
+
2907082
+
Steptoe/Morex(BxF)
+
AD_SCRI_97.CEL
+
+
+
OK
+
+
+
+
64
+
SM083
+
2907083
+
Steptoe/Morex(BxF)
+
AD_SCRI_89.CEL
+
+
+
OK
+
+
+
+
65
+
SM084
+
2907084
+
Morex/Steptoe(CxF)
+
AD_SCRI_155.CEL
+
+
+
OK
+
+
+
+
66
+
SM085
+
2907085
+
Morex/Steptoe(IxE)
+
AD_SCRI_149.CEL
+
0521-17_SetA17.CEL
+
SMmini
+
OK
+
OK
+
+
+
67
+
SM087
+
2907087
+
Steptoe/Morex(OxJ)
+
AD_SCRI_113.CEL
+
+
+
OK
+
+
+
+
68
+
SM088
+
2907088
+
Morex/Steptoe(CxF)
+
AD_SCRI_93.CEL
+
0521-18_SetA18.CEL
+
SMmini
+
OK
+
OK
+
+
+
69
+
SM089
+
2907089
+
Steptoe/Morex(OxJ)
+
AD_SCRI_148.CEL
+
0521-19_SetA19.CEL
+
SMmini
+
OK
+
OK
+
+
+
70
+
SM091
+
2907091
+
Morex/Steptoe(CxF)
+
AD_SCRI_110.CEL
+
+
+
OK
+
+
+
+
71
+
SM092
+
2907092
+
Steptoe/Morex(OxJ)
+
AD_SCRI_7.CEL
+
+
+
OK
+
+
+
+
72
+
SM093
+
2907093
+
Steptoe/Morex(BxF)
+
AD_SCRI_122.CEL
+
+
+
OK
+
+
+
+
73
+
SM094
+
2907094
+
Morex/Steptoe(CxF)
+
AD_SCRI_150.CEL
+
+
+
OK
+
+
+
+
74
+
SM097
+
2907097
+
Morex/Steptoe(CxF)
+
AD_SCRI_158.CEL
+
+
+
OK
+
+
+
+
75
+
SM098
+
2907098
+
Morex/Steptoe(CxF)
+
AD_SCRI_121.CEL
+
+
+
OK
+
+
+
+
76
+
SM099
+
2907099
+
Steptoe/Morex(QxG)
+
AD_SCRI_137.CEL
+
+
+
OK
+
+
+
+
77
+
SM103
+
2907103
+
Morex/Steptoe(IxE)
+
AD_SCRI_156.CEL
+
+
+
OK
+
+
+
+
78
+
SM104
+
2907104
+
Steptoe/Morex(BxH)
+
AD_SCRI_70.CEL
+
+
+
ERROR
+
+
+
+
79
+
SM105
+
2907105
+
Morex/Steptoe(IxE)
+
AD_SCRI_69.CEL
+
+
+
OK
+
+
+
+
80
+
SM110
+
2907110
+
Morex/Steptoe(CxF)
+
AD_SCRI_75.CEL
+
+
+
ERROR
+
+
+
+
81
+
SM112
+
2907112
+
Steptoe/Morex(BxF)
+
AD_SCRI_84.CEL
+
+
+
OK
+
+
+
+
82
+
SM116
+
2907116
+
Morex/Steptoe(CxF)
+
AD_SCRI_117.CEL
+
0521-20_SetA20.CEL
+
SMmini
+
OK
+
OK
+
+
+
83
+
SM120
+
2907120
+
Steptoe/Morex(OxJ)
+
AD_SCRI_138.CEL
+
+
+
OK
+
+
+
+
84
+
SM124
+
2907124
+
Steptoe/Morex(BxF)
+
AD_SCRI_146.CEL
+
+
+
OK
+
+
+
+
85
+
SM125
+
2907125
+
Morex/Steptoe(IxE)
+
AD_SCRI_43.CEL
+
+
+
OK
+
+
+
+
86
+
SM126
+
2907126
+
Steptoe/Morex(OxJ)
+
AD_SCRI_144_redo.CEL
+
+
+
OK
+
+
+
+
87
+
SM127
+
2907127
+
Steptoe/Morex(BxH)
+
AD_SCRI_129.CEL
+
+
+
OK
+
+
+
+
88
+
SM129
+
2907129
+
Steptoe/Morex(OxJ)
+
AD_SCRI_132.CEL
+
+
+
OK
+
+
+
+
89
+
SM130
+
2907130
+
Morex/Steptoe(CxF)
+
AD_SCRI_101.CEL
+
0521-21_SetA21.CEL
+
SMmini
+
OK
+
OK
+
+
+
90
+
SM131
+
2907131
+
Steptoe/Morex(OxJ)
+
AD_SCRI_102.CEL
+
+
+
OK
+
+
+
+
91
+
SM132
+
2907132
+
Steptoe/Morex(QxG)
+
AD_SCRI_4_redo.CEL
+
+
+
OK
+
+
+
+
92
+
SM133
+
2907133
+
Morex/Steptoe(CxF)
+
AD_SCRI_157.CEL
+
+
+
OK
+
+
+
+
93
+
SM134
+
2907134
+
Morex/Steptoe(IxE)
+
AD_SCRI_159.CEL
+
+
+
OK
+
+
+
+
94
+
SM135
+
2907135
+
Steptoe/Morex(BxF)
+
AD_SCRI_72.CEL
+
0521-22_SetA22.CEL
+
SMmini
+
OK
+
OK
+
+
+
95
+
SM136
+
2907136
+
Steptoe/Morex(QxG)
+
AD_SCRI_123.CEL
+
0521-23_SetA23.CEL
+
SMmini
+
OK
+
OK
+
+
+
96
+
SM137
+
2907137
+
Steptoe/Morex(BxH)
+
AD_SCRI_39.CEL
+
+
+
OK
+
+
+
+
97
+
SM139
+
2907139
+
Morex/Steptoe(CxF)
+
AD_SCRI_133.CEL
+
+
+
OK
+
+
+
+
98
+
SM140
+
2907140
+
Morex/Steptoe(CxF)
+
AD_SCRI_134.CEL
+
0521-24_SetA24.CEL
+
SMmini
+
OK
+
OK
+
+
+
99
+
SM141
+
2907141
+
Steptoe/Morex(BxH)
+
AD_SCRI_136.CEL
+
0521-25_SetA25.CEL
+
SMmini
+
OK
+
OK
+
+
+
100
+
SM142
+
2907142
+
Morex/Steptoe(IxE)
+
AD_SCRI_6.CEL
+
+
+
OK
+
+
+
+
101
+
SM143
+
2907143
+
Steptoe/Morex(BxH)
+
AD_SCRI_145.CEL
+
+
+
OK
+
+
+
+
102
+
SM144
+
2907144
+
Steptoe/Morex(BxF)
+
AD_SCRI_103.CEL
+
+
+
OK
+
+
+
+
103
+
SM145
+
2907145
+
Steptoe/Morex(QxG)
+
AD_SCRI_108.CEL
+
+
+
OK
+
+
+
+
104
+
SM146
+
2907146
+
Morex/Steptoe(BxF)
+
AD_SCRI_91.CEL
+
0521-26_SetA26.CEL
+
SMmini
+
OK
+
OK
+
+
+
105
+
SM147
+
2907147
+
Steptoe/Morex(OxJ)
+
AD_SCRI_139.CEL
+
+
+
OK
+
+
+
+
106
+
SM149
+
2907149
+
Steptoe/Morex(BxF)
+
AD_SCRI_131.CEL
+
+
+
ERROR
+
+
+
+
107
+
SM150
+
2907150
+
Morex/Steptoe(CxF)
+
AD_SCRI_37.CEL
+
+
+
OK
+
+
+
+
108
+
SM151
+
2907151
+
Morex/Steptoe(IxE)
+
AD_SCRI_28.CEL
+
+
+
OK
+
+
+
+
109
+
SM152
+
2907152
+
Steptoe/Morex(BxH)
+
AD_SCRI_9_redo.CEL
+
0521-27_SetA27.CEL
+
SMmini
+
OK
+
OK
+
+
+
110
+
SM153
+
2907153
+
Steptoe/Morex(BxH)
+
AD_SCRI_135.CEL
+
+
+
OK
+
+
+
+
111
+
SM154
+
2907154
+
Steptoe/Morex(BxH)
+
AD_SCRI_114.CEL
+
+
+
OK
+
+
+
+
112
+
SM155
+
2907155
+
Steptoe/Morex(BxH)
+
AD_SCRI_119.CEL
+
0521-28_SetA28.CEL
+
SMmini
+
OK
+
OK
+
+
+
113
+
SM156
+
2907156
+
Steptoe/Morex(BxH)
+
AD_SCRI_140.CEL
+
+
+
OK
+
+
+
+
114
+
SM157
+
2907157
+
Morex/Steptoe(CxF)
+
AD_SCRI_106_redo.CEL
+
+
+
OK
+
+
+
+
115
+
SM158
+
2907158
+
Morex/Steptoe(CxF)
+
AD_SCRI_65.CEL
+
+
+
OK
+
+
+
+
116
+
SM159
+
2907159
+
Morex/Steptoe(IxE)
+
AD_SCRI_168.CEL
+
+
+
OK
+
+
+
+
117
+
SM160
+
2907160
+
Steptoe/Morex(OxJ)
+
AD_SCRI_47.CEL
+
0521-29_SetA29.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
118
+
SM161
+
2907161
+
Steptoe/Morex(BxH)
+
AD_SCRI_76.CEL
+
+
+
ERROR
+
+
+
+
119
+
SM162
+
2907162
+
Morex/Steptoe(CxF)
+
AD_SCRI_147.CEL
+
+
+
OK
+
+
+
+
120
+
SM164
+
2907164
+
Steptoe/Morex(OxJ)
+
AD_SCRI_128.CEL
+
+
+
OK
+
+
+
+
121
+
SM165
+
2907165
+
Steptoe/Morex(BxH)
+
AD_SCRI_143.CEL
+
+
+
OK
+
OK
+
+
+
122
+
SM166
+
2907166
+
Morex/Steptoe(CxF)
+
AD_SCRI_115.CEL
+
+
+
OK
+
+
+
+
123
+
SM167
+
2907167
+
Steptoe/Morex(BxH)
+
AD_SCRI_127.CEL
+
0521-30_SetA30.CEL
+
SMmini
+
OK
+
OK
+
+
+
124
+
SM168
+
2907168
+
Steptoe/Morex(BxH)
+
AD_SCRI_130.CEL
+
+
+
OK
+
+
+
+
125
+
SM169
+
2907169
+
Morex/Steptoe(CxF)
+
AD_SCRI_118.CEL
+
0521-31_SetA31.CEL
+
SMmini
+
OK
+
OK
+
+
+
126
+
SM170
+
2907170
+
Steptoe/Morex(BxF)
+
AD_SCRI_151.CEL
+
+
+
OK
+
+
+
+
127
+
SM171
+
2907171
+
Steptoe/Morex(BxF)
+
AD_SCRI_165.CEL
+
+
+
ERROR
+
+
+
+
128
+
SM172
+
2907172
+
Steptoe/Morex(OxJ)
+
AD_SCRI_152.CEL
+
+
+
ERROR
+
+
+
+
129
+
SM173
+
2907173
+
Steptoe/Morex(OxJ)
+
AD_SCRI_104.CEL
+
0521-32_SetA32.CEL
+
SMmini
+
OK
+
OK
+
+
+
130
+
SM174
+
2907174
+
Steptoe/Morex(BxH)
+
AD_SCRI_154.CEL
+
+
+
OK
+
+
+
+
131
+
SM176
+
2907176
+
Morex/Steptoe(CxF)
+
AD_SCRI_141.CEL
+
+
+
OK
+
+
+
+
132
+
SM177
+
2907177
+
Morex/Steptoe(CxF)
+
AD_SCRI_111.CEL
+
0521-33_SetA33.CEL
+
SMmini
+
OK
+
OK
+
+
+
133
+
SM179
+
2907179
+
Morex/Steptoe(CxF)
+
AD_SCRI_166.CEL
+
+
+
OK
+
+
+
+
134
+
SM180
+
2907180
+
Morex/Steptoe(IxE)
+
AD_SCRI_161.CEL
+
+
+
OK
+
+
+
+
135
+
SM181
+
2907181
+
Morex/Steptoe(IxE)
+
AD_SCRI_162.CEL
+
+
+
OK
+
+
+
+
136
+
SM182
+
2907182
+
Morex/Steptoe(CxF)
+
AD_SCRI_163.CEL
+
+
+
OK
+
+
+
+
137
+
SM183
+
2907183
+
Morex/Steptoe(CxF)
+
AD_SCRI_164.CEL
+
+
+
OK
+
+
+
+
138
+
SM184
+
2907184
+
Morex/Steptoe(IxE)
+
AD_SCRI_160.CEL
+
0521-34_SetA34.CEL
+
SMmini
+
OK
+
OK
+
+
+
139
+
SM185
+
2907185
+
Morex/Steptoe(IxE)
+
AD_SCRI_167.CEL
+
+
+
OK
+
+
+
+
140
+
SM186
+
2907186
+
Morex/Steptoe(IxE)
+
AD_SCRI_62.CEL
+
+
+
OK
+
+
+
+
141
+
SM187
+
2907187
+
Morex/Steptoe(IxE)
+
AD_SCRI_61.CEL
+
+
+
OK
+
+
+
+
142
+
SM188
+
2907188
+
Morex/Steptoe(CxF)
+
AD_SCRI_63.CEL
+
+
+
OK
+
+
+
+
143
+
SM189
+
2907189
+
Steptoe/Morex(QxG)
+
AD_SCRI_80.CEL
+
+
+
OK
+
+
+
+
144
+
SM193
+
2907193
+
Morex/Steptoe(IxE)
+
AD_SCRI_36.CEL
+
+
+
OK
+
+
+
+
145
+
SM194
+
2907194
+
Steptoe/Morex(OxJ)
+
AD_SCRI_29.CEL
+
+
+
OK
+
+
+
+
146
+
SM196
+
2907196
+
Steptoe/Morex(BxF)
+
AD_SCRI_26.CEL
+
+
+
OK
+
+
+
+
147
+
SM197
+
2907197
+
Steptoe/Morex(BxF)
+
AD_SCRI_85.CEL
+
+
+
OK
+
+
+
+
148
+
SM198
+
2907198
+
Morex/Steptoe(IxE)
+
AD_SCRI_8.CEL
+
+
+
OK
+
+
+
+
149
+
SM199
+
2907199
+
Steptoe/Morex(BxF)
+
AD_SCRI_20.CEL
+
+
+
OK
+
+
+
+
150
+
SM200
+
2907200
+
Morex/Steptoe(IxE)
+
AD_SCRI_38.CEL
+
0521-35_SetA35.CEL
+
SMmini
+
OK
+
OK
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_17.CEL
+
0521-36_SetA36.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_66.CEL
+
0521-37_SetA37.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_68.CEL
+
0521-38_SetA38.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_116.CEL
+
0521-39_SetA39.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_14.CEL
+
0521-40_SetA40.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_67.CEL
+
0521-41_SetA41.CEL
+
+
+
+
+
+
+
+
+
About tissues used to generate this set of data:
+
+
+
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
+
+
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
+
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
+
+
+
+
+
+
RNA Sample Processing:
+
Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
+
+☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
+☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
+☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
+☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
+☐ While centrifuging, label new set of 15 ml tubes
+☐ Transfer supernatant to 15 ml centrifuge tube
+☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
+seconds, and incubate at room temperature for 5 minutes.
+☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
+☐ While centrifuging, label new 15 ml tubes
+☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
+☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
+☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
+☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
+4000 rpm for 15 minutes @ 4oC.
+☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
+☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
+☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
+few times.
+☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
+☐ Set water bath to 37oC.
+☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
+☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
+☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
+☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
+☐ Label 15 ml tubes from the kit and place midi columns in them
+☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
+☐ Discard the flow-through.
+☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
+incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
+☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
+gently, incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
+☐ Centrifuge again for another 5 min.
+☐ Label new 15 ml tubes from the kit.
+☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
+RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ To the same tube add again 250 ul H2O, incubate for 1 min.
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ Label two sets of 1.5 ml Eppendorf tubes.
+☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
+
+
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
+
+
Replication and Sample Balance:
+
3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
+
Experimental Design and Batch Structure:
+
+
+
+
+
+
Downloading complete data set:
+
+
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
+E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
+
+
+
+
About the array platform:
+
+
+
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
+
+
The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
+
+
+
+
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
+Barley1 Leaf MAS 5.0 SCRI (Dec 06)
+
+
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
+
+
+
Values below 0.01 were set to 0.01.
+
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
+
Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
+
+
+
+
+
+
+
+
Data source acknowledgment:
+
+
+
Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant
+
+
+SCR/910/04
+
+'The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
+
+
+
Contact address:
+
+
Arnis Druka
+
+Genetics Programme
+
+Scottish Crop Research Institute
+
+Invergowrie, Dundee DD2 5DA
+
+Angus, Scotland, United Kingdom
+
+Tel +44 01382 562731
+Fax +44 01382 568587
+adruka@scri.sari.ac.uk
+
+
+
References:
+
+
+
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64.
+ Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics,
+
+
+Jul;6(3):202-11.
+
+
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
+
+
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
+
+
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
+
+
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
+
+
+
+
+
+
+
About this text file:
+
+
+This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
Barley1 Leaf gcRMAn SCRI (Dec 06) - integrated probe set value for each gene has been calculated using RMA algorithm (Irizarry et al 2003). RMA ignores MM probe signals. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
+
+
Summary:
+
+
+
The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip.
+
+
+
About the lines used to generate this set of data:
+
+
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
+
+
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
+1)
+pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
+2)
+'minimapper' subset - MINI;
+3) lines that have expression data removed - ERROR:
+
+
+
+
Order #
+
Line ID
+
Permanent Oregon ID
+
Cross direction
+
CEL file names
+
Mini-mapper set
+
Error check
+
+
+
embryo data-set
+
leaf data-set
+
embryo data-set
+
leaf data-set
+
+
+
1
+
SM001
+
2907001
+
Steptoe/Morex(BxF)
+
AD_SCRI_82.CEL
+
+
+
OK
+
+
+
+
2
+
SM002
+
2907002
+
Steptoe/Morex(BxF)
+
AD_SCRI_1.CEL
+
+
+
OK
+
+
+
+
3
+
SM003
+
2907003
+
Morex/Steptoe(CxF)
+
AD_SCRI_19.CEL
+
+
+
OK
+
+
+
+
4
+
SM004
+
2907004
+
Morex/Steptoe(CxF)
+
AD_SCRI_3.CEL
+
0521-1_SetA1.CEL
+
SMmini
+
OK
+
OK
+
+
+
5
+
SM005
+
2907005
+
Steptoe/Morex(BxH)
+
AD_SCRI_88.CEL
+
+
+
OK
+
+
+
+
6
+
SM006
+
2907006
+
Morex/Steptoe(CxF)
+
AD_SCRI_48.CEL
+
+
+
OK
+
+
+
+
7
+
SM007
+
2907007
+
Steptoe/Morex(BxH)
+
AD_SCRI_35.CEL
+
0521-2_SetA2.CEL
+
SMmini
+
OK
+
OK
+
+
+
8
+
SM009
+
2907009
+
Steptoe/Morex(BxF)
+
AD_SCRI_2.CEL
+
+
+
OK
+
+
+
+
9
+
SM010
+
2907010
+
Morex/Steptoe(IxE)
+
AD_SCRI_42.CEL
+
+
+
OK
+
+
+
+
10
+
SM011
+
2907011
+
Steptoe/Morex(QxG)
+
AD_SCRI_10.CEL
+
+
+
OK
+
+
+
+
11
+
SM012
+
2907012
+
Morex/Steptoe(CxF)
+
AD_SCRI_45.CEL
+
0521-3_SetA3.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
12
+
SM013
+
2907013
+
Morex/Steptoe(IxE)
+
AD_SCRI_78.CEL
+
0521-4_SetA4.CEL
+
SMmini
+
ERROR
+
ERROR
+
+
+
13
+
SM014
+
2907014
+
Steptoe/Morex(BxH)
+
AD_SCRI_18.CEL
+
+
+
OK
+
+
+
+
14
+
SM015
+
2907015
+
Steptoe/Morex(BxH)
+
AD_SCRI_5.CEL
+
+
+
OK
+
+
+
+
15
+
SM016
+
2907016
+
Steptoe/Morex(BxH)
+
AD_SCRI_21.CEL
+
+
+
OK
+
+
+
+
16
+
SM020
+
2907020
+
Steptoe/Morex(OxJ)
+
AD_SCRI_77.CEL
+
+
+
OK
+
+
+
+
17
+
SM021
+
2907021
+
Morex/Steptoe(IxE)
+
AD_SCRI_30.CEL
+
+
+
OK
+
+
+
+
18
+
SM022
+
2907022
+
Morex/Steptoe(IxE)
+
AD_SCRI_31.CEL
+
0521-5_SetA5.CEL
+
SMmini
+
OK
+
OK
+
+
+
19
+
SM023
+
2907023
+
Steptoe/Morex(BxH)
+
AD_SCRI_32.CEL
+
+
+
OK
+
+
+
+
20
+
SM024
+
2907024
+
Morex/Steptoe(IxE)
+
AD_SCRI_33.CEL
+
0521-6_SetA6.CEL
+
SMmini
+
OK
+
OK
+
+
+
21
+
SM025
+
2907025
+
Morex/Steptoe(CxF)
+
AD_SCRI_34.CEL
+
+
+
OK
+
+
+
+
22
+
SM027
+
2907027
+
Steptoe/Morex(OxJ)
+
AD_SCRI_12.CEL
+
0521-7_SetA7.CEL
+
SMmini
+
OK
+
OK
+
+
+
23
+
SM030
+
2907030
+
Morex/Steptoe(IxE)
+
AD_SCRI_79.CEL
+
+
+
OK
+
+
+
+
24
+
SM031
+
2907031
+
Steptoe/Morex(OxJ)
+
AD_SCRI_16.CEL
+
+
+
OK
+
+
+
+
25
+
SM032
+
2907032
+
Morex/Steptoe(IxE)
+
AD_SCRI_13.CEL
+
+
+
OK
+
+
+
+
26
+
SM035
+
2907035
+
Morex/Steptoe(CxF)
+
AD_SCRI_15.CEL
+
+
+
ERROR
+
+
+
+
27
+
SM039
+
2907039
+
Morex/Steptoe(CxF)
+
AD_SCRI_41.CEL
+
+
+
OK
+
+
+
+
28
+
SM040
+
2907040
+
Steptoe/Morex(BxH)
+
AD_SCRI_83.CEL
+
+
+
OK
+
+
+
+
29
+
SM041
+
2907041
+
Steptoe/Morex(OxJ)
+
AD_SCRI_11_redo.CEL
+
0521-8_SetA8.CEL
+
SMmini
+
OK
+
OK
+
+
+
30
+
SM042
+
2907042
+
Morex/Steptoe(CxF)
+
AD_SCRI_57.CEL
+
+
+
OK
+
+
+
+
31
+
SM043
+
2907043
+
Morex/Steptoe(JxE)
+
AD_SCRI_49.CEL
+
0521-9_SetA9.CEL
+
SMmini
+
OK
+
OK
+
+
+
32
+
SM044
+
2907044
+
Steptoe/Morex(OxJ)
+
AD_SCRI_50.CEL
+
0521-10_SetA10.CEL
+
SMmini
+
OK
+
OK
+
+
+
33
+
SM045
+
2907045
+
Steptoe/Morex(BxH)
+
AD_SCRI_51.CEL
+
+
+
OK
+
+
+
+
34
+
SM046
+
2907046
+
Steptoe/Morex(OxJ)
+
AD_SCRI_52.CEL
+
0521-11_SetA11.CEL
+
SMmini
+
OK
+
OK
+
+
+
35
+
SM048
+
2907048
+
Steptoe/Morex(BxF)
+
AD_SCRI_53.CEL
+
+
+
ERROR
+
+
+
+
36
+
SM050
+
2907050
+
Morex/Steptoe(IxE)
+
AD_SCRI_46.CEL
+
+
+
OK
+
+
+
+
37
+
SM054
+
2907054
+
Morex/Steptoe(CxF)
+
AD_SCRI_60.CEL
+
+
+
OK
+
+
+
+
38
+
SM055
+
2907055
+
Steptoe/Morex(OxJ)
+
AD_SCRI_55.CEL
+
+
+
OK
+
+
+
+
39
+
SM056
+
2907056
+
Steptoe/Morex(BxH)
+
AD_SCRI_23.CEL
+
+
+
OK
+
+
+
+
40
+
SM057
+
2907057
+
Morex/Steptoe(CxF)
+
AD_SCRI_24.CEL
+
+
+
OK
+
+
+
+
41
+
SM058
+
2907058
+
Steptoe/Morex(BxF)
+
AD_SCRI_22.CEL
+
+
+
OK
+
+
+
+
42
+
SM059
+
2907059
+
Steptoe/Morex(BxH)
+
AD_SCRI_27.CEL
+
+
+
OK
+
+
+
+
43
+
SM061
+
2907061
+
Morex/Steptoe(LxF)
+
AD_SCRI_81.CEL
+
0521-12_SetA12.CEL
+
SMmini
+
OK
+
OK
+
+
+
44
+
SM062
+
2907062
+
Morex/Steptoe(CxF)
+
AD_SCRI_44.CEL
+
+
+
OK
+
+
+
+
45
+
SM063
+
2907063
+
Steptoe/Morex(OxJ)
+
AD_SCRI_40.CEL
+
0521-13_SetA13.CEL
+
SMmini
+
OK
+
OK
+
+
+
46
+
SM064
+
2907064
+
Morex/Steptoe(CxF)
+
AD_SCRI_87_redo.CEL
+
+
+
OK
+
+
+
+
47
+
SM065
+
2907065
+
Morex/Steptoe(CxF)
+
AD_SCRI_54.CEL
+
+
+
OK
+
+
+
+
48
+
SM067
+
2907067
+
Steptoe/Morex(OxJ)
+
AD_SCRI_73.CEL
+
+
+
OK
+
+
+
+
49
+
SM068
+
2907068
+
Steptoe/Morex(OxG)
+
AD_SCRI_56.CEL
+
+
+
ERROR
+
+
+
+
50
+
SM069
+
2907069
+
Steptoe/Morex(BxH)
+
AD_SCRI_71.CEL
+
+
+
OK
+
+
+
+
51
+
SM070
+
2907070
+
Steptoe/Morex(BxF)
+
AD_SCRI_64.CEL
+
+
+
OK
+
+
+
+
52
+
SM071
+
2907071
+
Steptoe/Morex(BxH)
+
AD_SCRI_58.CEL
+
+
+
OK
+
+
+
+
53
+
SM072
+
2907072
+
Morex/Steptoe(CxF)
+
AD_SCRI_59.CEL
+
+
+
OK
+
+
+
+
54
+
SM073
+
2907073
+
Steptoe/Morex(BxF)
+
AD_SCRI_74.CEL
+
0521-14_SetA14.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
55
+
SM074
+
2907074
+
Morex/Steptoe(CxF)
+
AD_SCRI_25.CEL
+
0521-15_SetA15.CEL
+
SMmini
+
OK
+
OK
+
+
+
56
+
SM075
+
2907075
+
Steptoe/Morex(QxG)
+
AD_SCRI_120.CEL
+
+
+
OK
+
+
+
+
57
+
SM076
+
2907076
+
Steptoe/Morex(BxF)
+
AD_SCRI_112.CEL
+
+
+
OK
+
+
+
+
58
+
SM077
+
2907077
+
Morex/Steptoe(CxF)
+
AD_SCRI_142.CEL
+
+
+
OK
+
+
+
+
59
+
SM078
+
2907078
+
Steptoe/Morex(BxF)
+
AD_SCRI_86.CEL
+
+
+
OK
+
+
+
+
60
+
SM079
+
2907079
+
Morex/Steptoe(CxF)
+
AD_SCRI_153.CEL
+
0521-16_SetA16.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
61
+
SM080
+
2907080
+
Steptoe/Morex(BxF)
+
AD_SCRI_107.CEL
+
+
+
OK
+
+
+
+
62
+
SM081
+
2907081
+
Morex/Steptoe(CxF)
+
AD_SCRI_105.CEL
+
+
+
OK
+
+
+
+
63
+
SM082
+
2907082
+
Steptoe/Morex(BxF)
+
AD_SCRI_97.CEL
+
+
+
OK
+
+
+
+
64
+
SM083
+
2907083
+
Steptoe/Morex(BxF)
+
AD_SCRI_89.CEL
+
+
+
OK
+
+
+
+
65
+
SM084
+
2907084
+
Morex/Steptoe(CxF)
+
AD_SCRI_155.CEL
+
+
+
OK
+
+
+
+
66
+
SM085
+
2907085
+
Morex/Steptoe(IxE)
+
AD_SCRI_149.CEL
+
0521-17_SetA17.CEL
+
SMmini
+
OK
+
OK
+
+
+
67
+
SM087
+
2907087
+
Steptoe/Morex(OxJ)
+
AD_SCRI_113.CEL
+
+
+
OK
+
+
+
+
68
+
SM088
+
2907088
+
Morex/Steptoe(CxF)
+
AD_SCRI_93.CEL
+
0521-18_SetA18.CEL
+
SMmini
+
OK
+
OK
+
+
+
69
+
SM089
+
2907089
+
Steptoe/Morex(OxJ)
+
AD_SCRI_148.CEL
+
0521-19_SetA19.CEL
+
SMmini
+
OK
+
OK
+
+
+
70
+
SM091
+
2907091
+
Morex/Steptoe(CxF)
+
AD_SCRI_110.CEL
+
+
+
OK
+
+
+
+
71
+
SM092
+
2907092
+
Steptoe/Morex(OxJ)
+
AD_SCRI_7.CEL
+
+
+
OK
+
+
+
+
72
+
SM093
+
2907093
+
Steptoe/Morex(BxF)
+
AD_SCRI_122.CEL
+
+
+
OK
+
+
+
+
73
+
SM094
+
2907094
+
Morex/Steptoe(CxF)
+
AD_SCRI_150.CEL
+
+
+
OK
+
+
+
+
74
+
SM097
+
2907097
+
Morex/Steptoe(CxF)
+
AD_SCRI_158.CEL
+
+
+
OK
+
+
+
+
75
+
SM098
+
2907098
+
Morex/Steptoe(CxF)
+
AD_SCRI_121.CEL
+
+
+
OK
+
+
+
+
76
+
SM099
+
2907099
+
Steptoe/Morex(QxG)
+
AD_SCRI_137.CEL
+
+
+
OK
+
+
+
+
77
+
SM103
+
2907103
+
Morex/Steptoe(IxE)
+
AD_SCRI_156.CEL
+
+
+
OK
+
+
+
+
78
+
SM104
+
2907104
+
Steptoe/Morex(BxH)
+
AD_SCRI_70.CEL
+
+
+
ERROR
+
+
+
+
79
+
SM105
+
2907105
+
Morex/Steptoe(IxE)
+
AD_SCRI_69.CEL
+
+
+
OK
+
+
+
+
80
+
SM110
+
2907110
+
Morex/Steptoe(CxF)
+
AD_SCRI_75.CEL
+
+
+
ERROR
+
+
+
+
81
+
SM112
+
2907112
+
Steptoe/Morex(BxF)
+
AD_SCRI_84.CEL
+
+
+
OK
+
+
+
+
82
+
SM116
+
2907116
+
Morex/Steptoe(CxF)
+
AD_SCRI_117.CEL
+
0521-20_SetA20.CEL
+
SMmini
+
OK
+
OK
+
+
+
83
+
SM120
+
2907120
+
Steptoe/Morex(OxJ)
+
AD_SCRI_138.CEL
+
+
+
OK
+
+
+
+
84
+
SM124
+
2907124
+
Steptoe/Morex(BxF)
+
AD_SCRI_146.CEL
+
+
+
OK
+
+
+
+
85
+
SM125
+
2907125
+
Morex/Steptoe(IxE)
+
AD_SCRI_43.CEL
+
+
+
OK
+
+
+
+
86
+
SM126
+
2907126
+
Steptoe/Morex(OxJ)
+
AD_SCRI_144_redo.CEL
+
+
+
OK
+
+
+
+
87
+
SM127
+
2907127
+
Steptoe/Morex(BxH)
+
AD_SCRI_129.CEL
+
+
+
OK
+
+
+
+
88
+
SM129
+
2907129
+
Steptoe/Morex(OxJ)
+
AD_SCRI_132.CEL
+
+
+
OK
+
+
+
+
89
+
SM130
+
2907130
+
Morex/Steptoe(CxF)
+
AD_SCRI_101.CEL
+
0521-21_SetA21.CEL
+
SMmini
+
OK
+
OK
+
+
+
90
+
SM131
+
2907131
+
Steptoe/Morex(OxJ)
+
AD_SCRI_102.CEL
+
+
+
OK
+
+
+
+
91
+
SM132
+
2907132
+
Steptoe/Morex(QxG)
+
AD_SCRI_4_redo.CEL
+
+
+
OK
+
+
+
+
92
+
SM133
+
2907133
+
Morex/Steptoe(CxF)
+
AD_SCRI_157.CEL
+
+
+
OK
+
+
+
+
93
+
SM134
+
2907134
+
Morex/Steptoe(IxE)
+
AD_SCRI_159.CEL
+
+
+
OK
+
+
+
+
94
+
SM135
+
2907135
+
Steptoe/Morex(BxF)
+
AD_SCRI_72.CEL
+
0521-22_SetA22.CEL
+
SMmini
+
OK
+
OK
+
+
+
95
+
SM136
+
2907136
+
Steptoe/Morex(QxG)
+
AD_SCRI_123.CEL
+
0521-23_SetA23.CEL
+
SMmini
+
OK
+
OK
+
+
+
96
+
SM137
+
2907137
+
Steptoe/Morex(BxH)
+
AD_SCRI_39.CEL
+
+
+
OK
+
+
+
+
97
+
SM139
+
2907139
+
Morex/Steptoe(CxF)
+
AD_SCRI_133.CEL
+
+
+
OK
+
+
+
+
98
+
SM140
+
2907140
+
Morex/Steptoe(CxF)
+
AD_SCRI_134.CEL
+
0521-24_SetA24.CEL
+
SMmini
+
OK
+
OK
+
+
+
99
+
SM141
+
2907141
+
Steptoe/Morex(BxH)
+
AD_SCRI_136.CEL
+
0521-25_SetA25.CEL
+
SMmini
+
OK
+
OK
+
+
+
100
+
SM142
+
2907142
+
Morex/Steptoe(IxE)
+
AD_SCRI_6.CEL
+
+
+
OK
+
+
+
+
101
+
SM143
+
2907143
+
Steptoe/Morex(BxH)
+
AD_SCRI_145.CEL
+
+
+
OK
+
+
+
+
102
+
SM144
+
2907144
+
Steptoe/Morex(BxF)
+
AD_SCRI_103.CEL
+
+
+
OK
+
+
+
+
103
+
SM145
+
2907145
+
Steptoe/Morex(QxG)
+
AD_SCRI_108.CEL
+
+
+
OK
+
+
+
+
104
+
SM146
+
2907146
+
Morex/Steptoe(BxF)
+
AD_SCRI_91.CEL
+
0521-26_SetA26.CEL
+
SMmini
+
OK
+
OK
+
+
+
105
+
SM147
+
2907147
+
Steptoe/Morex(OxJ)
+
AD_SCRI_139.CEL
+
+
+
OK
+
+
+
+
106
+
SM149
+
2907149
+
Steptoe/Morex(BxF)
+
AD_SCRI_131.CEL
+
+
+
ERROR
+
+
+
+
107
+
SM150
+
2907150
+
Morex/Steptoe(CxF)
+
AD_SCRI_37.CEL
+
+
+
OK
+
+
+
+
108
+
SM151
+
2907151
+
Morex/Steptoe(IxE)
+
AD_SCRI_28.CEL
+
+
+
OK
+
+
+
+
109
+
SM152
+
2907152
+
Steptoe/Morex(BxH)
+
AD_SCRI_9_redo.CEL
+
0521-27_SetA27.CEL
+
SMmini
+
OK
+
OK
+
+
+
110
+
SM153
+
2907153
+
Steptoe/Morex(BxH)
+
AD_SCRI_135.CEL
+
+
+
OK
+
+
+
+
111
+
SM154
+
2907154
+
Steptoe/Morex(BxH)
+
AD_SCRI_114.CEL
+
+
+
OK
+
+
+
+
112
+
SM155
+
2907155
+
Steptoe/Morex(BxH)
+
AD_SCRI_119.CEL
+
0521-28_SetA28.CEL
+
SMmini
+
OK
+
OK
+
+
+
113
+
SM156
+
2907156
+
Steptoe/Morex(BxH)
+
AD_SCRI_140.CEL
+
+
+
OK
+
+
+
+
114
+
SM157
+
2907157
+
Morex/Steptoe(CxF)
+
AD_SCRI_106_redo.CEL
+
+
+
OK
+
+
+
+
115
+
SM158
+
2907158
+
Morex/Steptoe(CxF)
+
AD_SCRI_65.CEL
+
+
+
OK
+
+
+
+
116
+
SM159
+
2907159
+
Morex/Steptoe(IxE)
+
AD_SCRI_168.CEL
+
+
+
OK
+
+
+
+
117
+
SM160
+
2907160
+
Steptoe/Morex(OxJ)
+
AD_SCRI_47.CEL
+
0521-29_SetA29.CEL
+
SMmini
+
OK
+
ERROR
+
+
+
118
+
SM161
+
2907161
+
Steptoe/Morex(BxH)
+
AD_SCRI_76.CEL
+
+
+
ERROR
+
+
+
+
119
+
SM162
+
2907162
+
Morex/Steptoe(CxF)
+
AD_SCRI_147.CEL
+
+
+
OK
+
+
+
+
120
+
SM164
+
2907164
+
Steptoe/Morex(OxJ)
+
AD_SCRI_128.CEL
+
+
+
OK
+
+
+
+
121
+
SM165
+
2907165
+
Steptoe/Morex(BxH)
+
AD_SCRI_143.CEL
+
+
+
OK
+
OK
+
+
+
122
+
SM166
+
2907166
+
Morex/Steptoe(CxF)
+
AD_SCRI_115.CEL
+
+
+
OK
+
+
+
+
123
+
SM167
+
2907167
+
Steptoe/Morex(BxH)
+
AD_SCRI_127.CEL
+
0521-30_SetA30.CEL
+
SMmini
+
OK
+
OK
+
+
+
124
+
SM168
+
2907168
+
Steptoe/Morex(BxH)
+
AD_SCRI_130.CEL
+
+
+
OK
+
+
+
+
125
+
SM169
+
2907169
+
Morex/Steptoe(CxF)
+
AD_SCRI_118.CEL
+
0521-31_SetA31.CEL
+
SMmini
+
OK
+
OK
+
+
+
126
+
SM170
+
2907170
+
Steptoe/Morex(BxF)
+
AD_SCRI_151.CEL
+
+
+
OK
+
+
+
+
127
+
SM171
+
2907171
+
Steptoe/Morex(BxF)
+
AD_SCRI_165.CEL
+
+
+
ERROR
+
+
+
+
128
+
SM172
+
2907172
+
Steptoe/Morex(OxJ)
+
AD_SCRI_152.CEL
+
+
+
ERROR
+
+
+
+
129
+
SM173
+
2907173
+
Steptoe/Morex(OxJ)
+
AD_SCRI_104.CEL
+
0521-32_SetA32.CEL
+
SMmini
+
OK
+
OK
+
+
+
130
+
SM174
+
2907174
+
Steptoe/Morex(BxH)
+
AD_SCRI_154.CEL
+
+
+
OK
+
+
+
+
131
+
SM176
+
2907176
+
Morex/Steptoe(CxF)
+
AD_SCRI_141.CEL
+
+
+
OK
+
+
+
+
132
+
SM177
+
2907177
+
Morex/Steptoe(CxF)
+
AD_SCRI_111.CEL
+
0521-33_SetA33.CEL
+
SMmini
+
OK
+
OK
+
+
+
133
+
SM179
+
2907179
+
Morex/Steptoe(CxF)
+
AD_SCRI_166.CEL
+
+
+
OK
+
+
+
+
134
+
SM180
+
2907180
+
Morex/Steptoe(IxE)
+
AD_SCRI_161.CEL
+
+
+
OK
+
+
+
+
135
+
SM181
+
2907181
+
Morex/Steptoe(IxE)
+
AD_SCRI_162.CEL
+
+
+
OK
+
+
+
+
136
+
SM182
+
2907182
+
Morex/Steptoe(CxF)
+
AD_SCRI_163.CEL
+
+
+
OK
+
+
+
+
137
+
SM183
+
2907183
+
Morex/Steptoe(CxF)
+
AD_SCRI_164.CEL
+
+
+
OK
+
+
+
+
138
+
SM184
+
2907184
+
Morex/Steptoe(IxE)
+
AD_SCRI_160.CEL
+
0521-34_SetA34.CEL
+
SMmini
+
OK
+
OK
+
+
+
139
+
SM185
+
2907185
+
Morex/Steptoe(IxE)
+
AD_SCRI_167.CEL
+
+
+
OK
+
+
+
+
140
+
SM186
+
2907186
+
Morex/Steptoe(IxE)
+
AD_SCRI_62.CEL
+
+
+
OK
+
+
+
+
141
+
SM187
+
2907187
+
Morex/Steptoe(IxE)
+
AD_SCRI_61.CEL
+
+
+
OK
+
+
+
+
142
+
SM188
+
2907188
+
Morex/Steptoe(CxF)
+
AD_SCRI_63.CEL
+
+
+
OK
+
+
+
+
143
+
SM189
+
2907189
+
Steptoe/Morex(QxG)
+
AD_SCRI_80.CEL
+
+
+
OK
+
+
+
+
144
+
SM193
+
2907193
+
Morex/Steptoe(IxE)
+
AD_SCRI_36.CEL
+
+
+
OK
+
+
+
+
145
+
SM194
+
2907194
+
Steptoe/Morex(OxJ)
+
AD_SCRI_29.CEL
+
+
+
OK
+
+
+
+
146
+
SM196
+
2907196
+
Steptoe/Morex(BxF)
+
AD_SCRI_26.CEL
+
+
+
OK
+
+
+
+
147
+
SM197
+
2907197
+
Steptoe/Morex(BxF)
+
AD_SCRI_85.CEL
+
+
+
OK
+
+
+
+
148
+
SM198
+
2907198
+
Morex/Steptoe(IxE)
+
AD_SCRI_8.CEL
+
+
+
OK
+
+
+
+
149
+
SM199
+
2907199
+
Steptoe/Morex(BxF)
+
AD_SCRI_20.CEL
+
+
+
OK
+
+
+
+
150
+
SM200
+
2907200
+
Morex/Steptoe(IxE)
+
AD_SCRI_38.CEL
+
0521-35_SetA35.CEL
+
SMmini
+
OK
+
OK
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_17.CEL
+
0521-36_SetA36.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_66.CEL
+
0521-37_SetA37.CEL
+
+
+
+
+
+
parent
+
Steptoe
+
+
+
AD_SCRI_68.CEL
+
0521-38_SetA38.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_116.CEL
+
0521-39_SetA39.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_14.CEL
+
0521-40_SetA40.CEL
+
+
+
+
+
+
parent
+
Morex
+
+
+
AD_SCRI_67.CEL
+
0521-41_SetA41.CEL
+
+
+
+
+
+
+
+
+
About tissues used to generate this set of data:
+
+
+
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
+
+
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
+
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
+
+
+
+
+
+
RNA Sample Processing:
+
Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
+
+☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
+☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
+☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
+☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
+☐ While centrifuging, label new set of 15 ml tubes
+☐ Transfer supernatant to 15 ml centrifuge tube
+☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
+seconds, and incubate at room temperature for 5 minutes.
+☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
+☐ While centrifuging, label new 15 ml tubes
+☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
+☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
+☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
+☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
+4000 rpm for 15 minutes @ 4oC.
+☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
+☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
+☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
+few times.
+☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
+☐ Set water bath to 37oC.
+☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
+☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
+☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
+☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
+☐ Label 15 ml tubes from the kit and place midi columns in them
+☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
+☐ Discard the flow-through.
+☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
+incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
+☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
+gently, incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
+☐ Centrifuge again for another 5 min.
+☐ Label new 15 ml tubes from the kit.
+☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
+RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ To the same tube add again 250 ul H2O, incubate for 1 min.
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ Label two sets of 1.5 ml Eppendorf tubes.
+☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
+
+
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
+
+
Replication and Sample Balance:
+
3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
+
Experimental Design and Batch Structure:
+
+
+
+
+
+
Downloading complete data set:
+
+
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
+E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
+
+
+
+
About the array platform:
+
+
+
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
+
+
The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
+
+
+
+
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
+Barley1 Leaf MAS 5.0 SCRI (Dec 06)
+
+
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
+
+
+
Values below 0.01 were set to 0.01.
+
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
+
Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
+
+
+
+
+
+
+
+
Data source acknowledgment:
+
+
+
Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant
+
+
+SCR/910/04
+
+'The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
+
+
+
Contact address:
+
+
Arnis Druka
+
+Genetics Programme
+
+Scottish Crop Research Institute
+
+Invergowrie, Dundee DD2 5DA
+
+Angus, Scotland, United Kingdom
+
+Tel +44 01382 562731
+Fax +44 01382 568587
+adruka@scri.sari.ac.uk
+
+
+
References:
+
+
+
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64.
+ Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics,
+
+
+Jul;6(3):202-11.
+
+
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
+
+
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
+
+
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
+
+
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
+
+
+
+
+
+
+
About this text file:
+
+
+This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
+The Genotype database of August 2005 lists genotypes for 194 MIT microsatellite markers and 110 F2 animals used in combination with the Phenotypes and Liver transcriptome databases for mapping quantitative trait loci. To review a complete list of these genotypes type in the wildcard character * in the ANY search field. You can also search more selectively for markers using this general syntax Mb=(Chr1 50 150) to find all markers on Chr 1 between 50 and 150 Mb. This marker set includes genotypes for all 60 selected animals whose liver mRNAs were quantified using the Affymetrix M430A and B arrays, as well as an additional 50 F2 ob/ob animals from the same cross.
+
+
+
+
About the cases used to generate this set of data:
+
+
The 110 F2-ob/ob mice were from a mapping panel that we created to map diabetes related physiological phenotypes (Stoehr et al. 2000). These F2-ob/ob mice were also used to map mRNA abundance traits derived by quantitative real-time RT-PCR (Lan et al. 2003). The sixty F2-ob/ob mice that were used to generate microarray-derived mRNA abundance traits were selected from the 110 mice based on a selective phenotyping algorithm (Jin et al. 2004). The F2-ob/ob mice were housed at weaning at the University of Wisconsin-Madison animal care facility on a 12-h light/dark cycle. Mice were provided Purina Formulab Chow 5008 (6.5% fat) and acidified water ad libitum. Mice were killed at 14 weeks of age by CO2 asphyxiation after a 4-hour fast. The livers, along with other tissues, were immediately foil wrapped and frozen in liquid nitrogen, and subsequently transferred to -80 °C freezers for storage.
+
+
About the marker set:
+
All 110 mice were genotyped at 194 MIT microsatellite markers separated an average of approximately 10 cM apart across the entire genome (Y chromsome, excepted). The maximum distance between markers wass less than 30 cM. The genotyping error-check routine implemented within R/qtl (Broman et al. 2003) showed no likely errors at p <0.01 probability.
+
+
+
+
+
+
Data source acknowledgment:
+
This project was supported in part by NIH/NIDDK 5803701, NIH/NIDDK 66369-01 and American Diabetes Association 7-03-IG-01 to Alan D. Attie, USDA CSREES grants to the University of Wisconsin-Madison to Brian S. Yandell, and HHMI grant A-53-1200-4 to Christina Kendziorski.
+
+
+
+
+
Information about this text file:
+
This text file originally generated by RWW and Alan Attie, August 20, 2005.
+
+The Phenotypes database of August 2005 provides quantitative trait data for 24 phenotypes from a set of 110 F2 animals generated by crossing strains C57BL/6J and BTBR. All F2s are homozygous for the obese (ob) allele of leptin (Lep) on Chr 6. Data were generated at the University of Wisconsin by Alan Attie and colleagues (Stoehr et al. 2000; Lan et al. 2003). This data release complement the liver transcriptome data described in the paper of Lan and colleagues (in submission, 2005). Traits include body weight, insulin and blood sugar levels, and rtPCR results. To review a complete list of the 24 phenotypes simply type in the wildcard character * in the ANY search field. This data set includes values for all 60 selected animals whose liver mRNA has been quantified using the Affymetrix M430A and B arrays, as well as an addition 50 F2 ob/ob animals from the same cross.
+
+
+
+
The 110 F2-ob/ob mice were chosen from a larger mapping panel that we created to map diabetes related physiological phenotypes (Stoehr et al. 2000). All 110 of this subsetwere used to map mRNA abundance traits derived by quantitative real-time RT-PCR (Lan et al. 2003).
+
+
+
+
Data source acknowledgment:
+
This project was supported in part by NIH/NIDDK 5803701, NIH/NIDDK 66369-01 and American Diabetes Association 7-03-IG-01 to Alan D. Attie, USDA CSREES grants to the University of Wisconsin-Madison to Brian S. Yandell, and HHMI grant A-53-1200-4 to Christina Kendziorski.
+
+
+
+
+
Information about this text file:
+
This text file originally generated by RWW and Alan Attie, August 20, 2005.
+
+This March 2004 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A microarrays. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
+
+
+
+
+
About the cases used to generate this set of data:
+
+
Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
+
+
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
+
+
+
About the tissue used to generate these data:
+
+
Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
+
+
+
About the arrays:
+
All 56 430A arrays used in this project were purchased at one time and had the same Affymetrix lot number.
+
+The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
+
+
+
+
+
+
+
Order
+
+
+
+CaseID
+
+
+
ArrayID
+
+
+
+Side
+
+
+
+
+
+CageID
+
+
+
+
+Sex
+
+
+
+
1
20
FL10
L
H1
F
+
2
2
FL11
L
H2
F
+
3
5
FL12
L
H3
F
+
4
63
FL13
L
H4
F
+
5
6
FL14
L
K2
F
+
6
10
FL15
L
Q2
F
+
7
52
FL2
L
E1
F
+
8
53
FL3
L
E2
F
+
9
42
FL4
L
E3
F
+
10
31
FL5
L
E4
F
+
11
14
FL6
L
F1
M
+
12
48
FL7
L
F2
F
+
13
60
FL8
L
F3
M
+
14
54
FL9
L
F4
F
+
15
35
FR10
R
K3
F
+
16
11
FR11
R
O1
F
+
17
21
FR12
R
O2
F
+
18
23
FR13
R
Q1
F
+
19
15
FR14
R
Q3
F
+
20
4
FR15
R
Q4
F
+
21
41
FR2
R
A2
F
+
22
44
FR3
R
A3
F
+
23
37
FR4
R
C1
F
+
24
8
FR5
R
C2
F
+
25
19
FR6
R
C3
F
+
26
40
FR7
R
C4
F
+
27
62
FR8
R
D2
M
+
28
39
FR9
R
D3
F
+
29
13
ML1
L
B1
M
+
30
22
ML10
L
L2
M
+
31
38
ML11
L
L4
M
+
32
43
ML12
L
M1
M
+
33
58
ML13
L
N2
M
+
34
7
ML14
L
R1
M
+
35
30
ML15
L
R3
M
+
36
46
ML3
L
G1
M
+
37
57
ML4
L
G2
M
+
38
51
ML5
L
I1
M
+
39
27
ML6
L
I2
M
+
40
50
ML7
L
J2
M
+
41
16
FL1
L
O2
M
+
42
3
ML9
L
L1
M
+
43
47
MR10
R
R2
M
+
44
56
MR11
R
S1
M
+
45
1
MR12
R
S2
M
+
46
55
MR13
R
T1
M
+
47
34
MR14
R
U1
M
+
48
25
MR15
R
U2
M
+
49
59
MR2
R
J1
M
+
50
32
MR3
R
M2
M
+
51
24
MR4
R
M3
M
+
52
12
MR5
R
M4
M
+
53
9
MR6
R
N1
M
+
54
36
MR7
R
N3
M
+
55
28
MR8
R
P1
M
+
56
33
MR9
R
P2
M
+
+
+
+
+
+
About the marker set:
+
+
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
+
+
+
+
About data processing:
+
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
+
+
+
Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
+
+
Step 2: We took the log2 of each probe signal.
+
+
Step 3: We computed the Z score for each signal within array.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
+
+
+
+Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
+
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
Data source acknowledgment:
+
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
+
+Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
+
+
+
+
References:
+
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
+
+This March 2004 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix U74Av2 microarrays. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
+
+
+
+
+
About the cases used to generate this set of data:
+
+
Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
+
+
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
+
+
+
About the tissue used to generate these data:
+
+
Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
+
+
+
About the arrays:
+
All 56 430A arrays used in this project were purchased at one time and had the same Affymetrix lot number.
+
+The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
+
+
+
+
+
+
+
Order
+
+
+
+ CaseID
+
+
+
ArrayID
+
+
+
+ Side
+
+
+
+
+
+ CageID
+
+
+
+
+ Sex
+
+
+
+
1
20
FL10
L
H1
F
+
2
2
FL11
L
H2
F
+
3
5
FL12
L
H3
F
+
4
63
FL13
L
H4
F
+
5
6
FL14
L
K2
F
+
6
10
FL15
L
Q2
F
+
7
52
FL2
L
E1
F
+
8
53
FL3
L
E2
F
+
9
42
FL4
L
E3
F
+
10
31
FL5
L
E4
F
+
11
14
FL6
L
F1
M
+
12
48
FL7
L
F2
F
+
13
60
FL8
L
F3
M
+
14
54
FL9
L
F4
F
+
15
35
FR10
R
K3
F
+
16
11
FR11
R
O1
F
+
17
21
FR12
R
O2
F
+
18
23
FR13
R
Q1
F
+
19
15
FR14
R
Q3
F
+
20
4
FR15
R
Q4
F
+
21
41
FR2
R
A2
F
+
22
44
FR3
R
A3
F
+
23
37
FR4
R
C1
F
+
24
8
FR5
R
C2
F
+
25
19
FR6
R
C3
F
+
26
40
FR7
R
C4
F
+
27
62
FR8
R
D2
M
+
28
39
FR9
R
D3
F
+
29
13
ML1
L
B1
M
+
30
22
ML10
L
L2
M
+
31
38
ML11
L
L4
M
+
32
43
ML12
L
M1
M
+
33
58
ML13
L
N2
M
+
34
7
ML14
L
R1
M
+
35
30
ML15
L
R3
M
+
36
46
ML3
L
G1
M
+
37
57
ML4
L
G2
M
+
38
51
ML5
L
I1
M
+
39
27
ML6
L
I2
M
+
40
50
ML7
L
J2
M
+
41
16
FL1
L
O2
M
+
42
3
ML9
L
L1
M
+
43
47
MR10
R
R2
M
+
44
56
MR11
R
S1
M
+
45
1
MR12
R
S2
M
+
46
55
MR13
R
T1
M
+
47
34
MR14
R
U1
M
+
48
25
MR15
R
U2
M
+
49
59
MR2
R
J1
M
+
50
32
MR3
R
M2
M
+
51
24
MR4
R
M3
M
+
52
12
MR5
R
M4
M
+
53
9
MR6
R
N1
M
+
54
36
MR7
R
N3
M
+
55
28
MR8
R
P1
M
+
56
33
MR9
R
P2
M
+
+
+
+
+
+
About the marker set:
+
+
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
+
+
+
+
About data processing:
+
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
+
+
+
Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
+
+
Step 2: We took the log2 of each probe signal.
+
+
Step 3: We computed the Z score for each signal within array.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
+
+
+
+Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
+
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
Data source acknowledgment:
+
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
+
+Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
+
+
+
+
References:
+
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
+
+This March 2004 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A microarrays. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Position-Dependent Nearest Neighbor (PDNN) method developed by Zhang and colleagues (2003. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
+
+This data set was run as a single large batch with careful consideration to balancing samples by sex, age, and environment.
+
+
+
+
+
+
About the cases used to generate this set of data:
+
+
Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
+
+
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
+
+
+
About the tissue used to generate these data:
+
+
Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
+
+
+
About the arrays:
+
All 56 430A arrays used in this project were purchased at one time and had the same Affymetrix lot number.
+
+The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
+
+
+
+
+
+
+
Order
+
+
+
+CaseID
+
+
+
ArrayID
+
+
+
+Side
+
+
+
+
+
+CageID
+
+
+
+
+Sex
+
+
+
+
1
20
FL10
L
H1
F
+
2
2
FL11
L
H2
F
+
3
5
FL12
L
H3
F
+
4
63
FL13
L
H4
F
+
5
6
FL14
L
K2
F
+
6
10
FL15
L
Q2
F
+
7
52
FL2
L
E1
F
+
8
53
FL3
L
E2
F
+
9
42
FL4
L
E3
F
+
10
31
FL5
L
E4
F
+
11
14
FL6
L
F1
M
+
12
48
FL7
L
F2
F
+
13
60
FL8
L
F3
M
+
14
54
FL9
L
F4
F
+
15
35
FR10
R
K3
F
+
16
11
FR11
R
O1
F
+
17
21
FR12
R
O2
F
+
18
23
FR13
R
Q1
F
+
19
15
FR14
R
Q3
F
+
20
4
FR15
R
Q4
F
+
21
41
FR2
R
A2
F
+
22
44
FR3
R
A3
F
+
23
37
FR4
R
C1
F
+
24
8
FR5
R
C2
F
+
25
19
FR6
R
C3
F
+
26
40
FR7
R
C4
F
+
27
62
FR8
R
D2
M
+
28
39
FR9
R
D3
F
+
29
13
ML1
L
B1
M
+
30
22
ML10
L
L2
M
+
31
38
ML11
L
L4
M
+
32
43
ML12
L
M1
M
+
33
58
ML13
L
N2
M
+
34
7
ML14
L
R1
M
+
35
30
ML15
L
R3
M
+
36
46
ML3
L
G1
M
+
37
57
ML4
L
G2
M
+
38
51
ML5
L
I1
M
+
39
27
ML6
L
I2
M
+
40
50
ML7
L
J2
M
+
41
16
FL1
L
O2
M
+
42
3
ML9
L
L1
M
+
43
47
MR10
R
R2
M
+
44
56
MR11
R
S1
M
+
45
1
MR12
R
S2
M
+
46
55
MR13
R
T1
M
+
47
34
MR14
R
U1
M
+
48
25
MR15
R
U2
M
+
49
59
MR2
R
J1
M
+
50
32
MR3
R
M2
M
+
51
24
MR4
R
M3
M
+
52
12
MR5
R
M4
M
+
53
9
MR6
R
N1
M
+
54
36
MR7
R
N3
M
+
55
28
MR8
R
P1
M
+
56
33
MR9
R
P2
M
+
+
+
+
+
+
About the marker set:
+
+
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
+
+
+
+
About data processing:
+
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
+
+
+
Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
+
+
Step 2: We took the log2 of each probe signal.
+
+
Step 3: We computed the Z score for each signal within array.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
+
+
+
+Probe set data: The uncorrected, untransformed CEL files were subject to probe (low) level processing using both the RMA (Robust Multiarray Average; Irizarry et al. 2003) and PDNN (Position Dependent Nearest Neighbor; Zhang et al. 2003) methods because these two performed the best of four methods tested in a recent four inbred strain comparison using the M430A chip on whole brain samples (Hitzemann et al, submitted). RMA was implemented by the Affy package (11/24/03 version) within Bioconductor (http://www.bioconductor.org) and PDNN by the PerfectMatch v. 2.1 program from Li Zhang (PDNN ). For sake of comparison with other data sets, MAS 5 files have also been generated.
+
+
To better compare data sets, the same simple steps (1 through 6 above) were applied to PDNN and RMA values. Every microarray data set therefore has a mean expression of 8 units with a standard deviation of 2 units. A 1-unit difference therefore represents roughly a 2-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
+
+
+
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
Data source acknowledgment:
+
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
+
+Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
+
+
+
+
References:
+
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
+
+This March 2004 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A microarrays. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. To simplify comparison between transforms, RMA values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with effort to balance samples by sex, age, and environment.
+
+
+
+
About the cases used to generate this set of data:
+
+
Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
+
+
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
+
+
+
About the tissue used to generate these data:
+
+
Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
+
+
+
About the arrays:
+
All 56 430A arrays used in this project were purchased at one time and had the same Affymetrix lot number.
+
+The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
+
+
+
+
+
+
+
Order
+
+
+
+CaseID
+
+
+
ArrayID
+
+
+
+Side
+
+
+
+
+
+CageID
+
+
+
+
+Sex
+
+
+
+
1
20
FL10
L
H1
F
+
2
2
FL11
L
H2
F
+
3
5
FL12
L
H3
F
+
4
63
FL13
L
H4
F
+
5
6
FL14
L
K2
F
+
6
10
FL15
L
Q2
F
+
7
52
FL2
L
E1
F
+
8
53
FL3
L
E2
F
+
9
42
FL4
L
E3
F
+
10
31
FL5
L
E4
F
+
11
14
FL6
L
F1
M
+
12
48
FL7
L
F2
F
+
13
60
FL8
L
F3
M
+
14
54
FL9
L
F4
F
+
15
35
FR10
R
K3
F
+
16
11
FR11
R
O1
F
+
17
21
FR12
R
O2
F
+
18
23
FR13
R
Q1
F
+
19
15
FR14
R
Q3
F
+
20
4
FR15
R
Q4
F
+
21
41
FR2
R
A2
F
+
22
44
FR3
R
A3
F
+
23
37
FR4
R
C1
F
+
24
8
FR5
R
C2
F
+
25
19
FR6
R
C3
F
+
26
40
FR7
R
C4
F
+
27
62
FR8
R
D2
M
+
28
39
FR9
R
D3
F
+
29
13
ML1
L
B1
M
+
30
22
ML10
L
L2
M
+
31
38
ML11
L
L4
M
+
32
43
ML12
L
M1
M
+
33
58
ML13
L
N2
M
+
34
7
ML14
L
R1
M
+
35
30
ML15
L
R3
M
+
36
46
ML3
L
G1
M
+
37
57
ML4
L
G2
M
+
38
51
ML5
L
I1
M
+
39
27
ML6
L
I2
M
+
40
50
ML7
L
J2
M
+
41
16
FL1
L
O2
M
+
42
3
ML9
L
L1
M
+
43
47
MR10
R
R2
M
+
44
56
MR11
R
S1
M
+
45
1
MR12
R
S2
M
+
46
55
MR13
R
T1
M
+
47
34
MR14
R
U1
M
+
48
25
MR15
R
U2
M
+
49
59
MR2
R
J1
M
+
50
32
MR3
R
M2
M
+
51
24
MR4
R
M3
M
+
52
12
MR5
R
M4
M
+
53
9
MR6
R
N1
M
+
54
36
MR7
R
N3
M
+
55
28
MR8
R
P1
M
+
56
33
MR9
R
P2
M
+
+
+
+
+
+
About the marker set:
+
+
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
+
+
+
+
About data processing:
+
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
+
+
+
Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
+
+
Step 2: We took the log2 of each probe signal.
+
+
Step 3: We computed the Z score for each signal within array.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
+
+
+
+Probe set data: The uncorrected, untransformed CEL files were subject to probe (low) level processing using both the RMA (Robust Multiarray Average; Irizarry et al. 2003) and PDNN (Position Dependent Nearest Neighbor; Zhang et al. 2003) methods because these two performed the best of four methods tested in a recent four inbred strain comparison using the M430A chip on whole brain samples (Hitzemann et al, submitted). RMA was implemented by the Affy package (11/24/03 version) within Bioconductor (http://www.bioconductor.org) and PDNN by the PerfectMatch v. 2.1 program from Li Zhang (PDNN ). For sake of comparison with other data sets, MAS 5 files have also been generated.
+
+
To better compare data sets, the same simple steps (1 through 6 above) were applied to PDNN and RMA values. Every microarray data set therefore has a mean expression of 8 units with a standard deviation of 2 units. A 1-unit difference therefore represents roughly a 2-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
+
+
+
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
Data source acknowledgment:
+
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
+
+Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
+
+
+
+
References:
+
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
+
+This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
+
+
+
+
+
About the cases used to generate this set of data:
+
+
Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
+
+
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
+
+
+
About the tissue used to generate these data:
+
+
Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B array pairs.
+
+
+
About the arrays:
+
All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number.
+
+The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
+
+
+
+
+
+
+
Order
+
+
+
+CaseID
+
+
+
ArrayID
+
+
+
+Side
+
+
+
+
+
+CageID
+
+
+
+
+Sex
+
+
+
+
1
20
FL10
L
H1
F
+
2
2
FL11
L
H2
F
+
3
5
FL12
L
H3
F
+
4
63
FL13
L
H4
F
+
5
6
FL14
L
K2
F
+
6
10
FL15
L
Q2
F
+
7
52
FL2
L
E1
F
+
8
53
FL3
L
E2
F
+
9
42
FL4
L
E3
F
+
10
31
FL5
L
E4
F
+
11
14
FL6
L
F1
M
+
12
48
FL7
L
F2
F
+
13
60
FL8
L
F3
M
+
14
54
FL9
L
F4
F
+
15
35
FR10
R
K3
F
+
16
11
FR11
R
O1
F
+
17
21
FR12
R
O2
F
+
18
23
FR13
R
Q1
F
+
19
15
FR14
R
Q3
F
+
20
4
FR15
R
Q4
F
+
21
41
FR2
R
A2
F
+
22
44
FR3
R
A3
F
+
23
37
FR4
R
C1
F
+
24
8
FR5
R
C2
F
+
25
19
FR6
R
C3
F
+
26
40
FR7
R
C4
F
+
27
62
FR8
R
D2
M
+
28
39
FR9
R
D3
F
+
29
13
ML1
L
B1
M
+
30
22
ML10
L
L2
M
+
31
38
ML11
L
L4
M
+
32
43
ML12
L
M1
M
+
33
58
ML13
L
N2
M
+
34
7
ML14
L
R1
M
+
35
30
ML15
L
R3
M
+
36
46
ML3
L
G1
M
+
37
57
ML4
L
G2
M
+
38
51
ML5
L
I1
M
+
39
27
ML6
L
I2
M
+
40
50
ML7
L
J2
M
+
41
16
FL1
L
O2
M
+
42
3
ML9
L
L1
M
+
43
47
MR10
R
R2
M
+
44
56
MR11
R
S1
M
+
45
1
MR12
R
S2
M
+
46
55
MR13
R
T1
M
+
47
34
MR14
R
U1
M
+
48
25
MR15
R
U2
M
+
49
59
MR2
R
J1
M
+
50
32
MR3
R
M2
M
+
51
24
MR4
R
M3
M
+
52
12
MR5
R
M4
M
+
53
9
MR6
R
N1
M
+
54
36
MR7
R
N3
M
+
55
28
MR8
R
P1
M
+
56
33
MR9
R
P2
M
+
+
+
+
+
+
About the marker set:
+
+
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
+
+
+
+
About data processing:
+
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
+
+
+
Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
+
Step 2: We took the log base 2 of each probe signal.
+
+
Step 3: We computed the Z scores for each probe signal.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
+
+
Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
+
+
+
+Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
+
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
Data source acknowledgment:
+
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
+
+Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
+
+
+
+
References:
+
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
+
+This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Position-Dependent Nearest Neighbor (PDNN) method developed by Zhang and colleagues (2003. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
+
+This data set was run as a single large batch with careful consideration to balancing samples by sex, age, and environment.
+
+
+
+
+
+
About the cases used to generate this set of data:
+
+
Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
+
+
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
+
+
+
About the tissue used to generate these data:
+
+
Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
+
+
+
About the arrays:
+
All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number.
+
+The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
+
+
+
+
+
+
+
Order
+
+
+
+CaseID
+
+
+
ArrayID
+
+
+
+Side
+
+
+
+
+
+CageID
+
+
+
+
+Sex
+
+
+
+
1
20
FL10
L
H1
F
+
2
2
FL11
L
H2
F
+
3
5
FL12
L
H3
F
+
4
63
FL13
L
H4
F
+
5
6
FL14
L
K2
F
+
6
10
FL15
L
Q2
F
+
7
52
FL2
L
E1
F
+
8
53
FL3
L
E2
F
+
9
42
FL4
L
E3
F
+
10
31
FL5
L
E4
F
+
11
14
FL6
L
F1
M
+
12
48
FL7
L
F2
F
+
13
60
FL8
L
F3
M
+
14
54
FL9
L
F4
F
+
15
35
FR10
R
K3
F
+
16
11
FR11
R
O1
F
+
17
21
FR12
R
O2
F
+
18
23
FR13
R
Q1
F
+
19
15
FR14
R
Q3
F
+
20
4
FR15
R
Q4
F
+
21
41
FR2
R
A2
F
+
22
44
FR3
R
A3
F
+
23
37
FR4
R
C1
F
+
24
8
FR5
R
C2
F
+
25
19
FR6
R
C3
F
+
26
40
FR7
R
C4
F
+
27
62
FR8
R
D2
M
+
28
39
FR9
R
D3
F
+
29
13
ML1
L
B1
M
+
30
22
ML10
L
L2
M
+
31
38
ML11
L
L4
M
+
32
43
ML12
L
M1
M
+
33
58
ML13
L
N2
M
+
34
7
ML14
L
R1
M
+
35
30
ML15
L
R3
M
+
36
46
ML3
L
G1
M
+
37
57
ML4
L
G2
M
+
38
51
ML5
L
I1
M
+
39
27
ML6
L
I2
M
+
40
50
ML7
L
J2
M
+
41
16
FL1
L
O2
M
+
42
3
ML9
L
L1
M
+
43
47
MR10
R
R2
M
+
44
56
MR11
R
S1
M
+
45
1
MR12
R
S2
M
+
46
55
MR13
R
T1
M
+
47
34
MR14
R
U1
M
+
48
25
MR15
R
U2
M
+
49
59
MR2
R
J1
M
+
50
32
MR3
R
M2
M
+
51
24
MR4
R
M3
M
+
52
12
MR5
R
M4
M
+
53
9
MR6
R
N1
M
+
54
36
MR7
R
N3
M
+
55
28
MR8
R
P1
M
+
56
33
MR9
R
P2
M
+
+
+
+
+
+
About the marker set:
+
+
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
+
+
+
+
About data processing:
+
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
+
+
+
Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
+
Step 2: We took the log base 2 of each probe signal.
+
+
Step 3: We computed the Z scores for each probe signal.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
+
+
Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
+
+
+
+
+Probe set data: The uncorrected, untransformed CEL files were subject to probe (low) level processing using both the RMA (Robust Multiarray Average; Irizarry et al. 2003) and PDNN (Position Dependent Nearest Neighbor; Zhang et al. 2003) methods because these two performed the best of four methods tested in a recent four inbred strain comparison using the M430A chip on whole brain samples (Hitzemann et al, submitted). RMA was implemented by the Affy package (11/24/03 version) within Bioconductor (http://www.bioconductor.org) and PDNN by the PerfectMatch v. 2.3 program from Li Zhang (PDNN ). For sake of comparison with other data sets, MAS 5 files have also been generated.
+
+
To better compare data sets, the same simple steps (1 through 6 above) were applied to PDNN and RMA values. Every microarray data set therefore has a mean expression of 8 units with a standard deviation of 2 units. A 1-unit difference therefore represents roughly a 2-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
+
+
+
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
Data source acknowledgment:
+
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
+
+Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
+
+
+
+
References:
+
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
+
+This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. To simplify comparison between transforms, RMA values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with effort to balance samples by sex, age, and environment.
+
+
+
+
About the cases used to generate this set of data:
+
+
Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A and M430B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
+
+
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
+
+
+
About the tissue used to generate these data:
+
+
Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B arraya.
+
+
+
About the arrays:
+
All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number.
+
+The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
+
+
+
+
+
+
+
Order
+
+
+
+CaseID
+
+
+
ArrayID
+
+
+
+Side
+
+
+
+
+
+CageID
+
+
+
+
+Sex
+
+
+
+
1
20
FL10
L
H1
F
+
2
2
FL11
L
H2
F
+
3
5
FL12
L
H3
F
+
4
63
FL13
L
H4
F
+
5
6
FL14
L
K2
F
+
6
10
FL15
L
Q2
F
+
7
52
FL2
L
E1
F
+
8
53
FL3
L
E2
F
+
9
42
FL4
L
E3
F
+
10
31
FL5
L
E4
F
+
11
14
FL6
L
F1
M
+
12
48
FL7
L
F2
F
+
13
60
FL8
L
F3
M
+
14
54
FL9
L
F4
F
+
15
35
FR10
R
K3
F
+
16
11
FR11
R
O1
F
+
17
21
FR12
R
O2
F
+
18
23
FR13
R
Q1
F
+
19
15
FR14
R
Q3
F
+
20
4
FR15
R
Q4
F
+
21
41
FR2
R
A2
F
+
22
44
FR3
R
A3
F
+
23
37
FR4
R
C1
F
+
24
8
FR5
R
C2
F
+
25
19
FR6
R
C3
F
+
26
40
FR7
R
C4
F
+
27
62
FR8
R
D2
M
+
28
39
FR9
R
D3
F
+
29
13
ML1
L
B1
M
+
30
22
ML10
L
L2
M
+
31
38
ML11
L
L4
M
+
32
43
ML12
L
M1
M
+
33
58
ML13
L
N2
M
+
34
7
ML14
L
R1
M
+
35
30
ML15
L
R3
M
+
36
46
ML3
L
G1
M
+
37
57
ML4
L
G2
M
+
38
51
ML5
L
I1
M
+
39
27
ML6
L
I2
M
+
40
50
ML7
L
J2
M
+
41
16
FL1
L
O2
M
+
42
3
ML9
L
L1
M
+
43
47
MR10
R
R2
M
+
44
56
MR11
R
S1
M
+
45
1
MR12
R
S2
M
+
46
55
MR13
R
T1
M
+
47
34
MR14
R
U1
M
+
48
25
MR15
R
U2
M
+
49
59
MR2
R
J1
M
+
50
32
MR3
R
M2
M
+
51
24
MR4
R
M3
M
+
52
12
MR5
R
M4
M
+
53
9
MR6
R
N1
M
+
54
36
MR7
R
N3
M
+
55
28
MR8
R
P1
M
+
56
33
MR9
R
P2
M
+
+
+
+
+
+
About the marker set:
+
+
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
+
+
+
+
About data processing:
+
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
+
+
+
Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
+
Step 2: We took the log base 2 of each probe signal.
+
+
Step 3: We computed the Z scores for each probe signal.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
+
+
Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
+
+
+
+
+Probe set data: The uncorrected, untransformed CEL files were subject to probe (low) level processing using both the RMA (Robust Multiarray Average; Irizarry et al. 2003) and PDNN (Position Dependent Nearest Neighbor; Zhang et al. 2003) methods because these two performed the best of four methods tested in a recent four inbred strain comparison using the M430A chip on whole brain samples (Hitzemann et al, submitted). RMA was implemented by the Affy package (11/24/03 version) within Bioconductor (http://www.bioconductor.org) and PDNN by the PerfectMatch v. 2.3 program from Li Zhang (PDNN ). For sake of comparison with other data sets, MAS 5 files have also been generated.
+
+
To better compare data sets, the same simple steps (1 through 6 above) were applied to PDNN and RMA values. Every microarray data set therefore has a mean expression of 8 units with a standard deviation of 2 units. A 1-unit difference therefore represents roughly a 2-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
+
+
+
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
Data source acknowledgment:
+
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
+
+Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
+
+
+
+
References:
+
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
+
+A
+PhenoGen Informatics data set. Please cite: Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B (2006) Candidate genes and their regulatory elements: alcohol preference and tolerance. Mammalian Genome 17:669-688 Full Text PDF Version, Full Text HTML Version
+
+
+
+
+
Summary:
+
+
+This November 2006 data freeze provides estimates of mRNA expression in whole brains of BXD recombinant inbred strains and 20 common inbred strrains measured using Affymetrix MOE 430 v2 micorarrays. Data were generated at the University of Colorado at Denver and Health Science Center (UCDHSC) by Dr. Boris Tabakof and colleague. Single whole brain samples were hybridized to 248 individual arrays. Data were processed using the RMA protocol followed by a secondary quantile normalization at the probe set level and a scale and location adjustment to ensure an average expression level of 8 units and a standard deviation of 2 units for easy comparison to other transforms.
+
+
+
The
+PhenoGen Informatics web site provides additional analytic tools and transforms associated with these data.
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimates of gene expression for 50 genetically uniform lines of mice: C57BL/6J (B6 or simply B), DBA/2J (D2 or D), 30 BXD recombinant inbred (RI) strain derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations, and 18 other inbred strains of mice available from the Jackson Laboratory. All mice used were naïve males from 70-90 days old. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. Another significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
In this mRNA expression database we generally used stock obtained directly from The Jackson Laboratory between 2003 and 2005.
+
+
About the tissue used to generate these data:
+
+
+Naïve male mice were euthanized by CO2 exposure, and whole brains were removed and frozen on dry ice. Brains were stored at -70 deg C until used. The RNeasy Midi kit for lipid-rich tissues (Qiagen, Valencia, CA) was used to extract total RNA, and the RNeasy Mini kit (Qiagen) was used for cleanup. Biotin-labeled cRNA was obtained by in vitro transcription of the double-stranded cDNA that was originally synthesized from the total RNA. Each whole brain sample of biotin-labeled cRNA was fragmented and hybridized to a separate oligonucleotide array. After hybridization, the chips were stained with streptavidin-phycoerythrin conjugate and scanned using an Affymetrix GeneArray scanner.
+
+
+
+
+
+
+
+
+
+
+
Strain
+
Sample Number
+
Scale
+factor
+
Average
+background
+
Absent
+
Marginal
+
Present
+
Affy-bActin
+
Affy-GAPH
+
+
+
BXD1
+
1
+
0.343
+
65.57
+
45.5%
+
4.1%
+
50.4%
+
1.33
+
0.74
+
+
+
BXD1
+
2
+
0.362
+
68.26
+
46.9%
+
4.5%
+
48.6%
+
1.30
+
0.76
+
+
+
BXD1
+
3
+
0.375
+
66.19
+
46.9%
+
4.2%
+
48.9%
+
1.27
+
0.77
+
+
+
BXD1
+
4
+
0.408
+
57.16
+
45.0%
+
4.0%
+
51.1%
+
1.27
+
0.80
+
+
+
BXD2
+
1
+
0.270
+
60.53
+
44.0%
+
4.1%
+
51.8%
+
1.52
+
0.87
+
+
+
BXD2
+
2
+
0.280
+
67.57
+
45.0%
+
4.2%
+
50.8%
+
1.31
+
0.75
+
+
+
BXD2
+
3
+
0.295
+
67.03
+
45.2%
+
4.1%
+
50.7%
+
1.34
+
0.76
+
+
+
BXD2
+
4
+
0.209
+
99.86
+
50.0%
+
4.7%
+
45.3%
+
1.24
+
0.73
+
+
+
BXD2
+
5
+
0.246
+
73.28
+
46.2%
+
4.3%
+
49.5%
+
1.34
+
0.73
+
+
+
BXD5
+
1
+
0.249
+
75.34
+
47.3%
+
4.4%
+
48.3%
+
1.34
+
0.73
+
+
+
BXD5
+
2
+
0.306
+
70.11
+
47.5%
+
4.5%
+
47.9%
+
1.31
+
0.77
+
+
+
BXD5
+
3
+
0.265
+
64.80
+
44.8%
+
4.3%
+
50.9%
+
1.33
+
0.74
+
+
+
BXD5
+
4
+
0.282
+
66.04
+
45.5%
+
4.2%
+
50.4%
+
1.41
+
0.76
+
+
+
BXD5
+
5
+
0.216
+
71.87
+
46.0%
+
3.9%
+
50.1%
+
3.07
+
1.01
+
+
+
BXD6
+
1
+
0.294
+
66.72
+
45.8%
+
4.3%
+
49.9%
+
1.38
+
0.75
+
+
+
BXD6
+
2
+
0.304
+
62.83
+
45.8%
+
4.2%
+
50.0%
+
1.25
+
0.72
+
+
+
BXD6
+
3
+
0.301
+
61.80
+
45.3%
+
4.3%
+
50.5%
+
1.27
+
0.76
+
+
+
BXD6
+
5
+
0.273
+
67.04
+
44.4%
+
4.2%
+
51.4%
+
1.32
+
0.76
+
+
+
BXD6
+
6
+
0.272
+
66.39
+
45.4%
+
4.3%
+
50.3%
+
1.32
+
0.75
+
+
+
BXD8
+
1
+
0.207
+
81.90
+
44.0%
+
3.9%
+
52.1%
+
1.33
+
0.74
+
+
+
BXD8
+
2
+
0.254
+
70.19
+
44.0%
+
3.9%
+
52.0%
+
1.32
+
0.72
+
+
+
BXD8
+
3
+
0.300
+
72.61
+
46.0%
+
4.0%
+
50.0%
+
1.30
+
0.74
+
+
+
BXD8
+
4
+
0.457
+
52.63
+
39.5%
+
3.3%
+
57.2%
+
1.14
+
0.79
+
+
+
BXD8
+
5
+
0.381
+
55.09
+
41.2%
+
3.4%
+
55.4%
+
1.12
+
0.79
+
+
+
BXD9
+
1
+
0.349
+
90.32
+
48.5%
+
4.1%
+
47.4%
+
1.38
+
0.78
+
+
+
BXD9
+
2
+
0.241
+
86.66
+
51.2%
+
4.8%
+
44.0%
+
1.38
+
0.75
+
+
+
BXD9
+
3
+
0.284
+
67.21
+
47.2%
+
4.3%
+
48.5%
+
1.33
+
0.78
+
+
+
BXD9
+
4
+
0.303
+
64.47
+
46.9%
+
4.5%
+
48.6%
+
1.32
+
0.77
+
+
+
BXD9
+
5
+
0.351
+
59.40
+
47.4%
+
4.4%
+
48.2%
+
1.41
+
0.80
+
+
+
BXD9
+
6
+
0.312
+
63.41
+
46.3%
+
4.4%
+
49.4%
+
1.39
+
0.76
+
+
+
BXD11
+
1
+
0.267
+
61.85
+
44.6%
+
4.3%
+
51.1%
+
1.36
+
0.75
+
+
+
BXD11
+
2
+
0.317
+
63.76
+
45.3%
+
4.3%
+
50.4%
+
1.29
+
0.79
+
+
+
BXD11
+
3
+
0.306
+
59.35
+
44.8%
+
4.2%
+
51.0%
+
1.33
+
0.79
+
+
+
BXD11
+
4
+
0.223
+
98.84
+
51.1%
+
4.6%
+
44.3%
+
1.32
+
0.73
+
+
+
BXD11
+
5
+
0.292
+
65.03
+
45.4%
+
4.0%
+
50.5%
+
1.38
+
0.78
+
+
+
BXD12
+
1
+
0.357
+
54.50
+
42.5%
+
3.7%
+
53.8%
+
1.15
+
0.76
+
+
+
BXD12
+
2
+
0.379
+
55.05
+
42.7%
+
3.7%
+
53.6%
+
1.15
+
0.76
+
+
+
BXD12
+
3
+
0.347
+
56.34
+
43.2%
+
3.9%
+
52.9%
+
1.17
+
0.74
+
+
+
BXD12
+
4
+
0.541
+
65.16
+
43.1%
+
3.4%
+
53.6%
+
1.08
+
0.79
+
+
+
BXD12
+
5
+
0.178
+
96.04
+
43.4%
+
4.0%
+
52.7%
+
1.29
+
0.74
+
+
+
BXD12
+
6
+
0.234
+
67.32
+
43.0%
+
3.9%
+
53.0%
+
1.31
+
0.75
+
+
+
BXD12
+
7
+
0.255
+
68.41
+
42.7%
+
4.2%
+
53.2%
+
1.50
+
0.76
+
+
+
BXD13
+
1
+
0.285
+
59.51
+
45.8%
+
4.2%
+
49.9%
+
1.22
+
0.75
+
+
+
BXD13
+
2
+
0.275
+
67.19
+
44.9%
+
4.2%
+
50.9%
+
1.29
+
0.76
+
+
+
BXD13
+
3
+
0.277
+
66.05
+
45.7%
+
4.2%
+
50.2%
+
1.38
+
0.79
+
+
+
BXD13
+
4
+
0.214
+
82.73
+
48.6%
+
4.5%
+
46.9%
+
1.40
+
0.78
+
+
+
BXD13
+
5
+
0.237
+
71.73
+
46.0%
+
4.3%
+
49.7%
+
1.29
+
0.77
+
+
+
BXD13
+
6
+
0.308
+
57.58
+
47.2%
+
4.2%
+
48.6%
+
1.33
+
0.74
+
+
+
BXD14
+
2
+
0.372
+
58.42
+
46.8%
+
4.4%
+
48.8%
+
1.19
+
0.74
+
+
+
BXD14
+
3
+
0.354
+
57.39
+
45.0%
+
4.2%
+
50.8%
+
1.20
+
0.72
+
+
+
BXD14
+
4
+
0.296
+
64.96
+
45.7%
+
4.4%
+
49.9%
+
1.20
+
0.69
+
+
+
BXD14
+
5
+
0.257
+
66.46
+
44.9%
+
4.4%
+
50.8%
+
1.24
+
0.72
+
+
+
BXD14
+
6
+
0.418
+
54.03
+
47.4%
+
4.1%
+
48.5%
+
1.10
+
0.74
+
+
+
BXD15
+
1
+
0.396
+
58.77
+
43.6%
+
3.9%
+
52.5%
+
1.33
+
0.78
+
+
+
BXD15
+
2
+
0.270
+
151.42
+
52.7%
+
4.7%
+
42.6%
+
1.36
+
0.73
+
+
+
BXD15
+
3
+
0.366
+
70.26
+
44.7%
+
3.9%
+
51.4%
+
1.29
+
0.79
+
+
+
BXD15
+
4
+
0.407
+
53.40
+
43.6%
+
4.1%
+
52.4%
+
1.38
+
0.79
+
+
+
BXD16
+
1
+
0.388
+
48.98
+
43.7%
+
4.1%
+
52.2%
+
1.41
+
0.79
+
+
+
BXD16
+
2
+
0.353
+
55.48
+
43.7%
+
4.0%
+
52.3%
+
1.44
+
0.82
+
+
+
BXD16
+
3
+
0.339
+
61.60
+
45.3%
+
4.2%
+
50.5%
+
1.42
+
0.80
+
+
+
BXD16
+
4
+
0.240
+
95.15
+
50.4%
+
4.7%
+
44.9%
+
1.39
+
0.73
+
+
+
BXD16
+
5
+
0.270
+
70.63
+
46.3%
+
4.3%
+
49.4%
+
1.45
+
0.75
+
+
+
BXD16
+
6
+
0.281
+
72.99
+
47.0%
+
4.2%
+
48.8%
+
1.40
+
0.77
+
+
+
BXD18
+
1
+
0.384
+
59.78
+
45.4%
+
4.0%
+
50.6%
+
1.12
+
0.71
+
+
+
BXD18
+
2
+
0.288
+
93.67
+
49.5%
+
4.4%
+
46.1%
+
1.15
+
0.70
+
+
+
BXD18
+
3
+
0.286
+
89.64
+
45.2%
+
4.1%
+
50.8%
+
1.27
+
0.71
+
+
+
BXD18
+
4
+
0.294
+
69.85
+
44.0%
+
4.1%
+
51.8%
+
1.26
+
0.70
+
+
+
BXD18
+
5
+
0.417
+
59.80
+
47.0%
+
4.3%
+
48.7%
+
1.15
+
0.72
+
+
+
BXD18
+
6
+
0.373
+
65.30
+
45.9%
+
4.3%
+
49.8%
+
1.18
+
0.74
+
+
+
BXD19
+
1
+
0.364
+
59.35
+
46.7%
+
4.2%
+
49.1%
+
1.27
+
0.73
+
+
+
BXD19
+
2
+
0.419
+
59.77
+
46.8%
+
4.1%
+
49.1%
+
1.23
+
0.74
+
+
+
BXD19
+
3
+
0.303
+
62.66
+
46.0%
+
4.4%
+
49.6%
+
1.30
+
0.74
+
+
+
BXD19
+
4
+
0.280
+
91.00
+
51.8%
+
4.5%
+
43.7%
+
1.32
+
0.68
+
+
+
BXD19
+
5
+
0.303
+
66.18
+
47.1%
+
4.5%
+
48.4%
+
1.33
+
0.72
+
+
+
BXD19
+
6
+
0.389
+
63.61
+
47.5%
+
4.4%
+
48.1%
+
1.28
+
0.73
+
+
+
BXD21
+
1
+
0.350
+
75.93
+
44.9%
+
3.9%
+
51.3%
+
1.29
+
0.77
+
+
+
BXD21
+
2
+
0.338
+
59.00
+
43.8%
+
4.0%
+
52.1%
+
1.29
+
0.77
+
+
+
BXD21
+
3
+
0.304
+
59.94
+
44.9%
+
4.0%
+
51.2%
+
1.44
+
0.77
+
+
+
BXD21
+
4
+
0.235
+
94.44
+
51.0%
+
4.8%
+
44.2%
+
1.35
+
0.73
+
+
+
BXD21
+
5
+
0.310
+
64.22
+
46.9%
+
4.2%
+
48.9%
+
1.42
+
0.77
+
+
+
BXD22
+
1
+
0.363
+
58.10
+
45.3%
+
3.9%
+
50.8%
+
1.24
+
0.80
+
+
+
BXD22
+
2
+
0.385
+
55.58
+
44.5%
+
4.0%
+
51.5%
+
1.28
+
0.80
+
+
+
BXD22
+
3
+
0.345
+
61.03
+
46.8%
+
4.3%
+
48.9%
+
1.35
+
0.81
+
+
+
BXD22
+
4
+
0.242
+
85.36
+
53.6%
+
4.8%
+
41.6%
+
1.35
+
0.75
+
+
+
BXD22
+
5
+
0.316
+
62.02
+
47.3%
+
4.5%
+
48.2%
+
1.40
+
0.77
+
+
+
BXD22
+
6
+
0.325
+
66.38
+
47.5%
+
4.3%
+
48.2%
+
1.29
+
0.78
+
+
+
BXD23
+
1
+
0.276
+
75.99
+
45.3%
+
4.1%
+
50.6%
+
1.27
+
0.75
+
+
+
BXD23
+
2
+
0.333
+
81.76
+
47.9%
+
4.0%
+
48.1%
+
1.28
+
0.78
+
+
+
BXD23
+
3
+
0.275
+
102.46
+
47.4%
+
3.9%
+
48.8%
+
1.30
+
0.77
+
+
+
BXD23
+
4
+
0.178
+
115.83
+
50.2%
+
4.7%
+
45.2%
+
1.38
+
0.73
+
+
+
BXD23
+
5
+
0.258
+
92.38
+
47.6%
+
4.2%
+
48.2%
+
1.32
+
0.77
+
+
+
BXD23
+
6
+
0.256
+
88.23
+
46.3%
+
4.1%
+
49.5%
+
1.31
+
0.74
+
+
+
BXD24
+
1
+
0.348
+
71.69
+
44.9%
+
4.1%
+
51.1%
+
1.25
+
0.74
+
+
+
BXD24
+
2
+
0.324
+
74.05
+
44.3%
+
4.0%
+
51.7%
+
1.23
+
0.80
+
+
+
BXD24
+
3
+
0.401
+
64.08
+
45.6%
+
4.0%
+
50.4%
+
1.08
+
0.74
+
+
+
BXD24
+
4
+
0.246
+
82.84
+
45.7%
+
4.3%
+
50.0%
+
1.20
+
0.75
+
+
+
BXD24
+
6
+
0.389
+
54.28
+
44.3%
+
4.2%
+
51.5%
+
1.20
+
0.67
+
+
+
BXD27
+
1
+
0.507
+
50.08
+
43.6%
+
3.9%
+
52.5%
+
1.48
+
0.81
+
+
+
BXD27
+
2
+
0.468
+
51.29
+
44.0%
+
3.7%
+
52.3%
+
1.44
+
0.90
+
+
+
BXD27
+
3
+
0.526
+
49.67
+
43.5%
+
3.9%
+
52.6%
+
1.29
+
0.94
+
+
+
BXD27
+
4
+
0.537
+
48.92
+
43.5%
+
3.8%
+
52.8%
+
1.46
+
0.91
+
+
+
BXD28
+
1
+
0.284
+
51.58
+
44.6%
+
4.2%
+
51.2%
+
1.26
+
0.80
+
+
+
BXD28
+
2
+
0.322
+
50.16
+
44.9%
+
4.3%
+
50.8%
+
1.21
+
0.76
+
+
+
BXD28
+
3
+
0.397
+
50.97
+
45.9%
+
4.2%
+
49.9%
+
1.14
+
0.78
+
+
+
BXD28
+
4
+
0.330
+
74.26
+
51.4%
+
4.6%
+
44.0%
+
1.26
+
0.72
+
+
+
BXD28
+
5
+
0.284
+
52.34
+
44.3%
+
4.4%
+
51.3%
+
1.32
+
0.73
+
+
+
BXD28
+
6
+
0.349
+
57.14
+
47.8%
+
4.5%
+
47.7%
+
1.30
+
0.79
+
+
+
BXD29
+
1
+
0.422
+
58.68
+
44.0%
+
3.7%
+
52.3%
+
1.42
+
0.86
+
+
+
BXD29
+
3
+
0.400
+
58.72
+
43.1%
+
3.8%
+
53.2%
+
1.31
+
0.89
+
+
+
BXD29
+
5
+
0.365
+
61.79
+
46.9%
+
4.3%
+
48.8%
+
1.38
+
0.91
+
+
+
BXD31
+
1
+
0.379
+
51.10
+
45.8%
+
4.3%
+
50.0%
+
1.13
+
0.75
+
+
+
BXD31
+
2
+
0.333
+
48.64
+
43.7%
+
4.1%
+
52.2%
+
1.22
+
0.71
+
+
+
BXD31
+
3
+
0.519
+
47.71
+
48.2%
+
4.3%
+
47.5%
+
1.13
+
0.72
+
+
+
BXD31
+
4
+
0.243
+
75.24
+
48.6%
+
4.8%
+
46.6%
+
1.23
+
0.71
+
+
+
BXD31
+
5
+
0.325
+
53.19
+
46.9%
+
4.6%
+
48.6%
+
1.22
+
0.75
+
+
+
BXD31
+
6
+
0.320
+
46.98
+
44.5%
+
4.3%
+
51.2%
+
1.24
+
0.74
+
+
+
BXD32
+
1
+
0.256
+
70.43
+
45.4%
+
3.9%
+
50.8%
+
1.83
+
0.87
+
+
+
BXD32
+
2
+
0.288
+
67.44
+
44.5%
+
4.1%
+
51.4%
+
1.34
+
0.77
+
+
+
BXD32
+
3
+
0.361
+
58.13
+
44.4%
+
4.0%
+
51.6%
+
1.36
+
0.77
+
+
+
BXD32
+
4
+
0.367
+
61.39
+
44.7%
+
4.1%
+
51.2%
+
1.40
+
0.78
+
+
+
BXD32
+
5
+
0.324
+
68.04
+
45.6%
+
4.3%
+
50.1%
+
1.39
+
0.75
+
+
+
BXD32
+
6
+
0.266
+
95.49
+
50.8%
+
4.5%
+
44.6%
+
1.41
+
0.73
+
+
+
BXD33
+
1
+
0.344
+
61.65
+
44.9%
+
3.9%
+
51.2%
+
1.38
+
0.82
+
+
+
BXD33
+
2
+
0.356
+
61.04
+
44.7%
+
4.1%
+
51.2%
+
1.44
+
0.79
+
+
+
BXD33
+
4
+
0.385
+
59.92
+
44.1%
+
3.9%
+
52.0%
+
1.38
+
0.82
+
+
+
BXD34
+
1
+
0.297
+
91.13
+
52.1%
+
4.6%
+
43.3%
+
1.34
+
0.70
+
+
+
BXD34
+
2
+
0.508
+
51.79
+
44.8%
+
3.9%
+
51.3%
+
1.42
+
0.76
+
+
+
BXD34
+
3
+
0.284
+
85.33
+
50.7%
+
4.6%
+
44.7%
+
1.51
+
0.72
+
+
+
BXD34
+
4
+
0.297
+
61.95
+
44.9%
+
4.1%
+
51.0%
+
1.36
+
0.77
+
+
+
BXD34
+
5
+
0.516
+
56.02
+
46.3%
+
4.0%
+
49.7%
+
1.33
+
0.74
+
+
+
BXD34
+
6
+
0.545
+
54.46
+
45.2%
+
3.8%
+
51.0%
+
1.49
+
0.87
+
+
+
BXD36
+
1
+
0.435
+
62.74
+
48.1%
+
4.0%
+
47.8%
+
1.36
+
0.73
+
+
+
BXD36
+
2
+
0.333
+
71.24
+
48.8%
+
4.3%
+
46.8%
+
1.44
+
0.72
+
+
+
BXD36
+
3
+
0.320
+
72.97
+
48.3%
+
4.3%
+
47.4%
+
1.38
+
0.74
+
+
+
BXD36
+
4
+
0.391
+
73.58
+
49.5%
+
4.2%
+
46.3%
+
1.25
+
0.75
+
+
+
BXD38
+
1
+
0.303
+
87.68
+
39.2%
+
3.3%
+
57.5%
+
1.08
+
0.82
+
+
+
BXD38
+
2
+
0.343
+
61.39
+
39.7%
+
3.2%
+
57.1%
+
1.12
+
0.82
+
+
+
BXD38
+
3
+
0.453
+
67.19
+
41.2%
+
3.4%
+
55.4%
+
1.11
+
0.83
+
+
+
BXD38
+
4
+
0.424
+
64.36
+
41.6%
+
3.5%
+
55.0%
+
1.11
+
0.82
+
+
+
BXD39
+
1
+
0.357
+
64.36
+
47.3%
+
4.3%
+
48.3%
+
1.33
+
0.78
+
+
+
BXD39
+
2
+
0.332
+
60.23
+
46.5%
+
4.2%
+
49.3%
+
1.41
+
0.80
+
+
+
BXD39
+
3
+
0.331
+
65.27
+
46.2%
+
4.2%
+
49.6%
+
1.32
+
0.75
+
+
+
BXD39
+
4
+
0.362
+
62.60
+
45.5%
+
4.0%
+
50.5%
+
1.28
+
0.80
+
+
+
BXD39
+
5
+
0.347
+
58.97
+
46.1%
+
4.3%
+
49.7%
+
1.29
+
0.79
+
+
+
BXD39
+
6
+
0.327
+
63.12
+
46.2%
+
4.3%
+
49.6%
+
1.29
+
0.77
+
+
+
BXD40
+
1
+
0.371
+
60.01
+
45.2%
+
4.1%
+
50.7%
+
1.32
+
0.77
+
+
+
BXD40
+
2
+
0.245
+
84.69
+
49.1%
+
4.5%
+
46.4%
+
1.33
+
0.72
+
+
+
BXD40
+
3
+
0.324
+
64.17
+
46.8%
+
4.3%
+
48.8%
+
1.34
+
0.73
+
+
+
BXD40
+
4
+
0.280
+
63.97
+
45.1%
+
4.2%
+
50.7%
+
1.48
+
0.74
+
+
+
BXD40
+
5
+
0.271
+
69.40
+
45.9%
+
4.3%
+
49.8%
+
1.33
+
0.74
+
+
+
BXD40
+
6
+
0.307
+
59.99
+
45.5%
+
4.2%
+
50.4%
+
1.37
+
0.76
+
+
+
BXD42
+
1
+
0.424
+
53.91
+
45.1%
+
4.1%
+
50.8%
+
1.54
+
0.83
+
+
+
BXD42
+
2
+
0.216
+
92.34
+
46.7%
+
4.3%
+
49.1%
+
1.44
+
0.76
+
+
+
BXD42
+
3
+
0.249
+
84.52
+
45.7%
+
4.1%
+
50.2%
+
1.52
+
0.80
+
+
+
BXD42
+
5
+
0.236
+
85.29
+
46.2%
+
4.0%
+
49.8%
+
1.38
+
0.77
+
+
+
DBA/2J
+
1
+
0.313
+
79.69
+
46.8%
+
4.2%
+
49.0%
+
1.24
+
0.72
+
+
+
DBA/2J
+
2
+
0.294
+
82.27
+
46.5%
+
4.2%
+
49.3%
+
1.27
+
0.73
+
+
+
DBA/2J
+
3
+
0.349
+
78.58
+
47.8%
+
4.3%
+
47.8%
+
1.31
+
0.73
+
+
+
DBA/2J
+
4
+
0.389
+
72.02
+
48.0%
+
4.3%
+
47.7%
+
1.21
+
0.77
+
+
+
DBA/2J
+
5
+
0.362
+
66.73
+
46.5%
+
4.4%
+
49.1%
+
1.23
+
0.75
+
+
+
DBA/2J
+
6
+
0.341
+
79.88
+
46.7%
+
4.0%
+
49.4%
+
1.33
+
0.74
+
+
+
C57BL/6J
+
1
+
0.294
+
82.84
+
46.7%
+
4.1%
+
49.2%
+
1.23
+
0.76
+
+
+
C57BL/6J
+
2
+
0.242
+
80.40
+
43.1%
+
4.1%
+
52.8%
+
1.29
+
0.76
+
+
+
C57BL/6J
+
3
+
0.250
+
110.90
+
47.8%
+
4.0%
+
48.2%
+
1.32
+
0.76
+
+
+
C57BL/6J
+
4
+
0.289
+
101.88
+
47.5%
+
4.1%
+
48.4%
+
1.18
+
0.75
+
+
+
C57BL/6J
+
5
+
0.299
+
114.59
+
48.7%
+
4.1%
+
47.3%
+
1.13
+
0.74
+
+
+
C57BL/6J
+
6
+
0.251
+
105.90
+
45.8%
+
3.8%
+
50.4%
+
1.30
+
0.76
+
+
+
129P3/J
+
1
+
0.496
+
59.26
+
41.9%
+
3.5%
+
54.5%
+
1.28
+
0.79
+
+
+
129P3/J
+
2
+
0.550
+
50.83
+
42.0%
+
3.7%
+
54.3%
+
1.16
+
0.78
+
+
+
129P3/J
+
3
+
0.443
+
56.08
+
43.0%
+
3.8%
+
53.3%
+
1.22
+
0.73
+
+
+
129P3/J
+
4
+
0.521
+
58.92
+
44.8%
+
3.8%
+
51.4%
+
1.30
+
0.74
+
+
+
129P3/J
+
5
+
0.503
+
58.26
+
44.9%
+
3.8%
+
51.3%
+
1.32
+
0.74
+
+
+
129S1/SvImJ
+
1
+
0.311
+
66.76
+
47.8%
+
3.9%
+
48.3%
+
2.04
+
0.97
+
+
+
129S1/SvImJ
+
2
+
0.262
+
57.63
+
44.5%
+
3.9%
+
51.6%
+
1.61
+
0.81
+
+
+
129S1/SvImJ
+
3
+
0.322
+
62.67
+
45.3%
+
3.8%
+
50.9%
+
1.70
+
0.83
+
+
+
129S1/SvImJ
+
4
+
0.185
+
119.02
+
50.2%
+
4.4%
+
45.5%
+
1.66
+
0.75
+
+
+
A/J
+
1
+
0.453
+
51.85
+
42.6%
+
3.6%
+
53.8%
+
1.20
+
0.73
+
+
+
A/J
+
2
+
0.396
+
56.61
+
45.9%
+
3.9%
+
50.2%
+
1.21
+
0.76
+
+
+
A/J
+
3
+
0.421
+
62.34
+
47.0%
+
4.1%
+
48.8%
+
1.29
+
0.72
+
+
+
A/J
+
4
+
0.508
+
61.52
+
48.2%
+
4.1%
+
47.7%
+
1.22
+
0.74
+
+
+
AKR/J
+
1
+
0.331
+
54.70
+
41.7%
+
3.9%
+
54.4%
+
1.22
+
0.74
+
+
+
AKR/J
+
2
+
0.464
+
55.46
+
44.1%
+
3.7%
+
52.1%
+
1.30
+
0.76
+
+
+
AKR/J
+
4
+
0.444
+
53.62
+
47.6%
+
4.0%
+
48.4%
+
1.23
+
0.71
+
+
+
AKR/J
+
5
+
0.439
+
58.62
+
47.4%
+
4.3%
+
48.3%
+
1.23
+
0.70
+
+
+
BALB/cByJ
+
1
+
0.336
+
75.49
+
50.0%
+
4.1%
+
45.9%
+
1.54
+
0.82
+
+
+
BALB/cByJ
+
2
+
0.280
+
67.93
+
47.1%
+
4.3%
+
48.7%
+
1.43
+
0.76
+
+
+
BALB/cByJ
+
3
+
0.312
+
73.77
+
47.7%
+
4.1%
+
48.2%
+
1.79
+
0.92
+
+
+
BALB/cByJ
+
4
+
0.262
+
79.97
+
46.1%
+
4.1%
+
49.8%
+
1.38
+
0.79
+
+
+
BALB/cByJ
+
5
+
0.276
+
81.32
+
46.3%
+
4.1%
+
49.6%
+
1.34
+
0.79
+
+
+
BALB/cJ
+
1
+
0.591
+
54.25
+
43.2%
+
3.5%
+
53.3%
+
1.15
+
0.80
+
+
+
BALB/cJ
+
2
+
0.346
+
50.36
+
39.9%
+
3.3%
+
56.8%
+
1.20
+
0.77
+
+
+
BALB/cJ
+
3
+
0.333
+
52.79
+
40.4%
+
3.7%
+
55.9%
+
1.25
+
0.77
+
+
+
BALB/cJ
+
5
+
0.495
+
54.78
+
45.0%
+
3.7%
+
51.3%
+
1.15
+
0.72
+
+
+
BTBR T+tf/J
+
3
+
0.315
+
62.83
+
46.4%
+
4.1%
+
49.5%
+
1.38
+
0.78
+
+
+
BTBR T+tf/J
+
4
+
0.243
+
90.12
+
51.6%
+
4.8%
+
43.6%
+
1.31
+
0.75
+
+
+
BTBR T+tf/J
+
5
+
0.294
+
71.21
+
46.6%
+
4.3%
+
49.0%
+
1.41
+
0.77
+
+
+
BTBR T+tf/J
+
6
+
0.268
+
67.53
+
46.6%
+
4.2%
+
49.2%
+
1.32
+
0.75
+
+
+
BTBR T+tf/J
+
1
+
0.370
+
55.40
+
45.7%
+
4.1%
+
50.2%
+
1.41
+
0.75
+
+
+
BTBR T+tf/J
+
2
+
0.488
+
50.89
+
47.2%
+
4.2%
+
48.6%
+
1.36
+
0.75
+
+
+
C3H/HeJ
+
1
+
0.511
+
59.20
+
43.3%
+
3.4%
+
53.3%
+
1.17
+
0.83
+
+
+
C3H/HeJ
+
2
+
0.405
+
79.49
+
41.3%
+
3.3%
+
55.5%
+
1.18
+
0.83
+
+
+
C3H/HeJ
+
3
+
0.454
+
59.47
+
41.7%
+
3.5%
+
54.9%
+
1.16
+
0.81
+
+
+
C3H/HeJ
+
4
+
0.448
+
56.28
+
41.5%
+
3.5%
+
55.0%
+
1.16
+
0.79
+
+
+
C3H/HeJ
+
5
+
0.389
+
50.17
+
41.1%
+
3.6%
+
55.2%
+
1.24
+
0.79
+
+
+
C58/J
+
1
+
0.336
+
56.66
+
46.0%
+
4.2%
+
49.8%
+
1.29
+
0.73
+
+
+
C58/J
+
2
+
0.372
+
58.61
+
46.7%
+
4.3%
+
49.0%
+
1.21
+
0.71
+
+
+
C58/J
+
3
+
0.366
+
64.58
+
46.8%
+
4.2%
+
49.0%
+
1.20
+
0.72
+
+
+
C58/J
+
4
+
0.371
+
52.72
+
45.3%
+
4.1%
+
50.6%
+
1.24
+
0.72
+
+
+
CAST/EiJ
+
1
+
0.467
+
55.74
+
47.1%
+
3.8%
+
49.1%
+
1.39
+
0.79
+
+
+
CAST/EiJ
+
2
+
0.545
+
50.29
+
46.8%
+
3.8%
+
49.4%
+
1.34
+
0.84
+
+
+
CAST/EiJ
+
3
+
0.469
+
55.08
+
47.4%
+
4.0%
+
48.5%
+
1.32
+
0.76
+
+
+
CAST/EiJ
+
4
+
0.390
+
83.05
+
53.0%
+
4.4%
+
42.6%
+
1.36
+
0.72
+
+
+
CBA/J
+
1
+
0.292
+
67.25
+
44.9%
+
4.0%
+
51.2%
+
1.22
+
0.76
+
+
+
CBA/J
+
2
+
0.347
+
61.99
+
46.4%
+
4.0%
+
49.7%
+
1.25
+
0.82
+
+
+
CBA/J
+
3
+
0.305
+
62.16
+
46.3%
+
4.3%
+
49.4%
+
1.31
+
0.75
+
+
+
CBA/J
+
4
+
0.303
+
64.82
+
46.5%
+
4.0%
+
49.5%
+
1.34
+
0.76
+
+
+
CBA/J
+
5
+
0.313
+
64.15
+
45.3%
+
4.1%
+
50.7%
+
1.37
+
0.78
+
+
+
CBA/J
+
6
+
0.365
+
56.84
+
45.6%
+
4.1%
+
50.4%
+
1.31
+
0.76
+
+
+
FVB/NJ
+
1
+
0.497
+
63.99
+
44.2%
+
3.5%
+
52.3%
+
1.33
+
0.79
+
+
+
FVB/NJ
+
2
+
0.475
+
55.24
+
44.8%
+
3.8%
+
51.4%
+
1.33
+
0.74
+
+
+
FVB/NJ
+
3
+
0.527
+
56.07
+
42.6%
+
3.5%
+
53.9%
+
1.31
+
0.86
+
+
+
FVB/NJ
+
4
+
0.447
+
62.56
+
41.7%
+
3.5%
+
54.8%
+
1.24
+
0.82
+
+
+
KK/HIJ
+
1
+
0.309
+
93.54
+
49.6%
+
4.3%
+
46.1%
+
1.57
+
0.74
+
+
+
KK/HIJ
+
2
+
0.298
+
63.24
+
48.0%
+
4.4%
+
47.6%
+
1.37
+
0.72
+
+
+
KK/HIJ
+
4
+
0.223
+
93.03
+
44.7%
+
4.0%
+
51.3%
+
1.39
+
0.74
+
+
+
KK/HIJ
+
5
+
0.153
+
136.67
+
51.9%
+
4.6%
+
43.5%
+
1.24
+
0.71
+
+
+
MOLF/EiJ
+
1
+
0.339
+
67.11
+
49.1%
+
4.3%
+
46.6%
+
1.55
+
0.83
+
+
+
MOLF/EiJ
+
2
+
0.319
+
80.73
+
49.1%
+
4.2%
+
46.7%
+
1.52
+
0.78
+
+
+
MOLF/EiJ
+
3
+
0.380
+
69.03
+
49.1%
+
4.2%
+
46.7%
+
1.29
+
0.82
+
+
+
MOLF/EiJ
+
4
+
0.238
+
95.19
+
48.7%
+
4.1%
+
47.2%
+
1.35
+
0.79
+
+
+
NOD/LtJ
+
1
+
0.356
+
78.42
+
49.1%
+
4.2%
+
46.7%
+
1.35
+
0.76
+
+
+
NOD/LtJ
+
2
+
0.422
+
59.71
+
47.4%
+
4.0%
+
48.5%
+
1.25
+
0.73
+
+
+
NOD/LtJ
+
3
+
0.377
+
77.84
+
49.8%
+
4.0%
+
46.2%
+
1.24
+
0.75
+
+
+
NOD/LtJ
+
4
+
0.535
+
60.86
+
50.6%
+
4.4%
+
45.0%
+
1.28
+
0.74
+
+
+
NOD/LtJ
+
5
+
0.336
+
74.58
+
46.6%
+
3.9%
+
49.5%
+
1.32
+
0.72
+
+
+
NZW/LacJ
+
2
+
0.442
+
50.31
+
44.6%
+
4.1%
+
51.3%
+
1.33
+
0.82
+
+
+
NZW/LacJ
+
3
+
0.331
+
56.86
+
44.2%
+
4.0%
+
51.7%
+
1.60
+
0.78
+
+
+
NZW/LacJ
+
4
+
0.338
+
55.23
+
44.1%
+
4.0%
+
51.9%
+
1.31
+
0.78
+
+
+
NZW/LacJ
+
5
+
0.351
+
56.90
+
49.3%
+
4.3%
+
46.5%
+
1.30
+
0.75
+
+
+
PWD/PhJ
+
1
+
0.444
+
57.65
+
47.2%
+
3.9%
+
48.9%
+
1.62
+
0.78
+
+
+
PWD/PhJ
+
2
+
0.328
+
67.58
+
47.3%
+
4.2%
+
48.5%
+
1.36
+
0.76
+
+
+
PWD/PhJ
+
3
+
0.322
+
73.90
+
47.5%
+
4.0%
+
48.5%
+
1.46
+
0.81
+
+
+
PWD/PhJ
+
4
+
0.271
+
75.79
+
46.1%
+
4.0%
+
50.0%
+
1.39
+
0.79
+
+
+
PWD/PhJ
+
5
+
0.191
+
144.73
+
57.7%
+
5.0%
+
37.3%
+
1.36
+
0.67
+
+
+
SJL/J
+
1
+
0.528
+
54.58
+
41.1%
+
3.4%
+
55.4%
+
1.16
+
0.80
+
+
+
SJL/J
+
3
+
0.663
+
56.21
+
41.8%
+
3.3%
+
55.0%
+
1.22
+
0.75
+
+
+
SJL/J
+
4
+
0.646
+
52.96
+
40.5%
+
3.2%
+
56.3%
+
1.13
+
0.81
+
+
+
SJL/J
+
5
+
0.639
+
61.91
+
44.8%
+
3.4%
+
51.9%
+
1.37
+
0.79
+
+
+
+
+
About the array platform:
+
+
+Affymetrix MOE430v2 GeneChip: The expression data were generated using 248 MOE430v2 arrays. The chromosomal locations of MOE430v2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6). This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
About data processing:
+
+Probe set data: The expression data were processed by Laura Saba (UCDHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed within the rma function in R. This data set includes further normalization to produce final estimates of expression that can be compared directly to the other transforms.
+
+
+
This includes an initial quantile normalization on the RMA normalized probe set data followed by a transformation to force an array average of 8 units and stabilized standard deviation of 2 units within each array. Please see Bolstad and colleagues (2003) for a helpful comparison of RMA and two other methods of processing Affymetrix array data sets.
+
+
+
Expression estimates (strain averages) range from a low of about 3.8 for probe set 1457109_x_at to a high of 15 for Gapdh (probe set 1418625_s_at). The mean expression of 8.0 actually represents a relatively low value of expression (roughly 250 on the original scale) because it is the average of all transcripts on the array, including those that are not expressed. Nonetheless, it is possible to obtain good signal down to very low values. For example, probe set 1437432_a_at (Trim12) has an average expression of 4.56 (extremely low), but it still is associated with a strong QTL (LRS of 45) precisely at the location of the parent gene (Chr 7 at 104 Mb). This demonstrates unequivocally that the small strain differences in expression of Trim12 measured by probe set 1437432_a_at is not noise but is generated by true allelic differences in Trim12 mRNA binding to the arrays.
+
+
Data source acknowledgment:
+
Data was generated with funds from NIAAA for Gene Array Technology Center (AA013162) and from the NIAAA Integrated Neuroinformatics Resource for Alcoholism (AA013524).
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, August for UTHSC Brain mRNA U74Av2 (Aug05) RMA. Updated for UC Denver Whole Brain M430v2 BXD (Nov06) RMA Data by LMS, November 2006. Updated by RWW, Feb 2008.
+
+This March 2004 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 100 arrays. Data were processed using the dChip protocol of Li and Wong and are presented without further modification (the original Perfect Match-Mismatch transform data set: PMMM Orig). In general, the dChip transforms do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HWT1PM) for this particular application.
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
About data processing:
+
+
Probe set data: The expression data were transformed by Cheng Li (Harvard University). The original expression values in the CEL files produced by MAS 5 were read into dChip to generate PM and PMMM data sets.
+
+
When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
+
+
+
+
+
About the array probe set names:
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
_f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
_s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
_g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
_r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
_i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
_st (sense target): Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW and EJC, March 2004. Updated by RWW, October 29, 2004.
+
+This March 2004 data freeze provides estimate of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 100 arrays. Data were processed using the dChip protocol of Li and Wong and are presented without further modification (Perfect Match: PM Orig). For this application, the dChip transforms do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
About data processing:
+
+
Probe set data: The expression data were transformed by Cheng Li (Harvard University). The original expression values in the CEL files produced by MAS 5 were read into the dChip to generate the PM transform and the PMMM transform data sets. Probe set data are averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. This data set does not include further normalization.
+
+
+
+
+
About the array probe set names:
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match (PM) probes and 16 mismatch controls (MM). Each set of these probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target): Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, and EJC, March 2004. Updated by RWW, October 29, Nov 5, 2004.
+
+This March 2004 data freeze provides estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 100 arrays. Data were processed using the RMA protocol and are presented without further modification (RMA Orig).
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current data set (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. All animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, and the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and to download indivdiual data files. You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify UCSC and Verify Emsembl links in the Trait Data and Editing Form (see buttons to the right side of the Location line).
+
+
+
+
About data processing:
+
+
+Probe set data: The expression data were processed by Bing Zhang (Oak Ridge National Laboratory) and Yanhua Qu (UTHSC). The original CEL files produced by the Affymetrix analysis software were read into the R environment (Ihaka and Gentleman 1996). Data were normalized using the Robust Multichip Average (RMA) method of background correction, quantile normalization, and summarization of cell signal intensity (Irrizary et al. 2003). Probe set intensities were log2 transformed. Probe set data are averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. This data set does not include further normalization ("RMA Orig" as in original). Please see Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
+
+
+
+
About the array probe set names:
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match (PM) probes and 16 mismatch controls (MM). Each set of these probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target) : Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, and EJC, March 2004. Updated by RWW, Oct 29, Nov 6, 2004.
+
+This March 2004 data freeze provides estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 100 arrays. Data were processed using the RMA protocol and are presented without further modification (RMA Orig).
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current data set (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. All animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, and the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and to download indivdiual data files. You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify UCSC and Verify Emsembl links in the Trait Data and Editing Form (see buttons to the right side of the Location line).
+
+
+
+
About data processing:
+
+
+Probe set data: The expression data were processed by Bing Zhang (Oak Ridge National Laboratory) and Yanhua Qu (UTHSC). The original CEL files produced by the Affymetrix analysis software were read into the R environment (Ihaka and Gentleman 1996). Data were normalized using the Robust Multichip Average (RMA) method of background correction, quantile normalization, and summarization of cell signal intensity (Irrizary et al. 2003). Probe set intensities were log2 transformed. Probe set data are averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. This data set does not include further normalization ("RMA Orig" as in original). Please see Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
+
+
+
+
About the array probe set names:
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match (PM) probes and 16 mismatch controls (MM). Each set of these probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target) : Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, and EJC, March 2004. Updated by RWW, Oct 29, Nov 6, 2004.
+
+This April 05 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n = 3) to 100 arrays. Data were processed using the S-score software of Zhang et al. 2002 and Kerns et al. 2003. The S- score method centers expression of every probe set at 0. The signal values are therefore strain deviations in Z score units from the grand mean based on all arrays.
+
+
+
+
+
About the cases used to generate this set of data:
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
+
+
+About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
+
+About the array platform:
+
+
+
+Affymetrix U74Av2 GeneChip Annotation: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify UCSC and Verify Emsembllinks in the Trait Data and Editing Form (see buttons to the right side of the Location line).
+
+You can download the original BLAT output file that we have generated for the U74Av2 platform. The GeneNetwork includes a filtered subset of these data.
+
+
+
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match (PM) probes and 16 mismatch controls (MM). Each set of these probe has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target) : Designates a sense target; almost always generated in error.
+Probe set data: The expression data were processed by RWW and Yanhua Qu at UTHSC to generate MAS 5 CEL files. These were then analyzed using the S-score algorithm (Zhang et al., 2002; Kerns et al., 2003) by Robnet Kerns and Michael Miles (Virginia Commonwealth University). The original CEL files produced by the Affymetrix analysis software were normalized for whole chip intensity and read into a version of the S-score software that produces an averaged CEL file across all arrays. This aveCEL was then used as the denominator to produce S-scores by pairwise analysis of all arrays. Probe set data are averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. This data set does not include further normalization.
+
+
Regarding the S-score (from the Miles Lab web site): "The significance-score algorithm (S-score) was developed in our laboratory by Dr. Li Zhang. This produces a score for a comparison of the expression of a gene between two samples (e.g. control and "treated"). The S-score produces a robust measure of expression changes by weighting oligonucleotide pairs according to their signal strength above empirically determined noise levels. The procedure produces scores centered around "0" (no change) with a standard deviation of 1. Thus, scores >2 or <-2 from a single comparison have, on average, a 95% chance of being "real changes" in terms of the chip hybridization. This does not, however, imply that they are biologically reproducible."
+
+
+
+
+
+
+Data source acknowledgment:
+
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
+This text file originally generated by RWW, KFM, and Mike Miles, April 14, 2005. Updated by RWW, April 15, 2005.
+
+
+
+This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target) : Designates a sense target; almost always generated in error.
Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
+
+
Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
+
+
Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
+
+
Step 3: We computed the Z scores for each cell value.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
+
+
Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
+
+
+
+Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
+
+
+
Data source acknowledgment:
+
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
+This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
+
+
+
+This August 2005 data freeze provides estimate of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 250 brain samples from 33 strains were hybridized in small pools (n=3) to 83 arrays. Data were processed using the PDNN method of Zhang. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), the B6D2 F1 intercross progeny, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
About data processing:
+
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
+
+
+
Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
+
+
Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
+
+
Step 3: We computed the Z scores for each cell value.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
+
+
Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
+
+
+
+
Probe set data: The expression data were transformed by Li Zhang (MD Anderson Cancer Center). The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
+
+
PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
+
+
When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
+
+
+
+
+
About the array probe set names:
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target): Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, August 2005.
+
+This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. The variance of each array has been stabilized to 2 units for easy comparison to other transforms (see below).
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current data set (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
About data processing:
+
Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
+
+
Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
+
+
Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
+
+
Step 3: We computed the Z scores for each cell value.
+
+
Step 4: We multiplied all Z scores by 2.
+
+
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
+
+
Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
+
+
Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
+
+
+Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples.
+
+
This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized variance of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
+
+
+
About the array probe set names:
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target) : Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, August 2005.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 83 arrays were used: 67 were female pools and 16 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).
+
+
+
About data processing:
+
+
Probe set data from the .TXT file: These .TXT files
+were generated using the dChip
+including perfect match data.
+
+
Step 1: We added an offset of 1 to the .TXT expression values
+for each cell to ensure that all values could be logged without
+generating negative values.
+
Step 2: We took the log base 2 of each cell.
+
Step 3: We computed the Z-score for each cell.
+
Step 4: We multiplied all Z scores by 2.
+
Step 5: We added 8 to the value of all Z-scores. The consequence
+of this simple set of transformations is to produce a set of Z-scores
+that have a mean of 8, a variance of 4, and a standard deviation
+of 2. The advantage of this modified Z-score is that a two-fold
+difference in expression level corresponds approximately to a 1
+unit difference.
+
Step 6: We computed the arithmetic mean of the values for the
+set of microarrays for each of the individual strains.
+
+
Every microarray data set therefore has a mean expression of 8 with
+a standard deviation of 2. A 1-unit difference therefor represents
+roughly a two-fold difference in expression level. Expression levels
+below 5 are usually close to background noise levels.
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
+
+
+
+
+
+
+
Strain
+
+
+
+Age
+
+
+
Strain
+
+
+
+Age
+
+
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+
C57BL/6J (B6)
+
♂♂♂
+
♀
+
♀
+
DBA/2J (D2)
+
♀
+
♂♂♀
+
+
+
+
B6D2F1 (F1)
+
♀ ♀
+
♀
+
+
BXD1
+
♀♀
+
+
♀
+
+
+
BXD2
+
♂
+
♀
+
♀
+
BXD5
+
♂♂♀
+
+
+
+
+
BXD6
+
♀
+
+
+
BXD8
+
♀
+
♂♀
+
+
+
+
BXD9
+
♂
+
♀
+
♀
+
BXD11
+
♀♀
+
+
♀
+
+
+
BXD12
+
+
♂
+
♀
+
BXD13
+
♀
+
+
+
+
+
BXD14
+
+
♀♀
+
♀
+
BXD15
+
♀
+
+
♀
+
+
+
BXD16
+
♀
+
♀
+
+
BXD18
+
♀
+
♂
+
♀
+
+
+
BXD19
+
♀
+
♀
+
♀
+
BXD21
+
♀♀
+
♂♂
+
+
+
+
BXD22
+
♀
+
♀♀
+
+
BXD23
+
♀
+
+
+
+
+
BXD24
+
♀♀
+
+
♀
+
BXD25
+
♀♀
+
♀♀
+
+
+
+
BXD27
+
+
+
♀♀
+
BXD28
+
♀
+
♀
+
♀
+
+
+
BXD29
+
♂
+
+
♀
+
BXD31
+
♀♀
+
♀♀
+
+
+
+
BXD32
+
♀
+
♂♀
+
♀
+
BXD33
+
♂♀
+
♀
+
+
+
+
BXD34
+
♂♀
+
♀
+
+
BXD38
+
♂♀♀
+
+
+
+
+
BXD39
+
♂♀
+
♂
+
+
BXD40
+
♂♂♀
+
+
+
+
+
BXD42
+
♂♂ ♀
+
+
+
BXD67
+
♀ ♀
+
+
+
+
+
BXD68
+
♀ ♀
+
♂
+
+
+
+
+
+
+
+
+
+
+
+
About the tissue used to generate these data:
+
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 83 arrays were used: 67 were female pools and 16 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).
+
+
+
About data processing:
+
+
Probe set data from the .TXT file: These .TXT files
+were generated using the dChip
+including perfect match and Missmatch data.
+
+
Step 1: We added an offset of 5000 to the .TXT expression values
+for each cell to ensure that all values could be logged without
+generating negative values.
+
Step 2: We took the log base 2 of each cell.
+
Step 3: We computed the Z-score for each cell.
+
Step 4: We multiplied all Z scores by 2.
+
Step 5: We added 8 to the value of all Z-scores. The consequence
+of this simple set of transformations is to produce a set of Z-scores
+that have a mean of 8, a variance of 4, and a standard deviation
+of 2. The advantage of this modified Z-score is that a two-fold
+difference in expression level corresponds approximately to a 1
+unit difference.
+
Step 6.1: We computed the arithmetic mean of the values for the
+set of microarrays for each of technical duplicate for the individual
+strains.
+
Step 6.2: We computed the arithmetic mean of the values for the
+set of microarrays for each of the individual strains.
+
+
Every microarray data set therefore has a mean expression of 8 with
+a standard deviation of 2. A 1-unit difference therefor represents
+roughly a two-fold difference in expression level. Expression levels
+below 5 are usually close to background noise levels.
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be 45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
+
+
+
+
+
+
+
Strain
+
+
+
+Age
+
+
+
Strain
+
+
+
+Age
+
+
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+
C57BL/6J (B6)
+
♂♂♂
+
♀
+
♀
+
DBA/2J (D2)
+
♀
+
♂♂♀
+
+
+
+
B6D2F1 (F1)
+
♀ ♀
+
♀
+
+
BXD1
+
♀♀
+
+
♀
+
+
+
BXD2
+
♂
+
♀
+
♀
+
BXD5
+
♂♂♀
+
+
+
+
+
BXD6
+
♀
+
+
+
BXD8
+
♀
+
♂♀
+
+
+
+
BXD9
+
♂
+
♀
+
♀
+
BXD11
+
♀♀
+
+
♀
+
+
+
BXD12
+
+
♂
+
♀
+
BXD13
+
♀
+
+
+
+
+
BXD14
+
+
♀♀
+
♀
+
BXD15
+
♀
+
+
♀
+
+
+
BXD16
+
♀
+
♀
+
+
BXD18
+
♀
+
♂
+
♀
+
+
+
BXD19
+
♀
+
♀
+
♀
+
BXD21
+
♀♀
+
♂♂
+
+
+
+
BXD22
+
♀
+
♀♀
+
+
BXD23
+
♀
+
+
+
+
+
BXD24
+
♀♀
+
+
♀
+
BXD25
+
♀♀
+
♀♀
+
+
+
+
BXD27
+
+
+
♀♀
+
BXD28
+
♀
+
♀
+
♀
+
+
+
BXD29
+
♂
+
+
♀
+
BXD31
+
♀♀
+
♀♀
+
+
+
+
BXD32
+
♀
+
♂♀
+
♀
+
BXD33
+
♂♀
+
♀
+
+
+
+
BXD34
+
♂♀
+
♀
+
+
BXD38
+
♂♀♀
+
+
+
+
+
BXD39
+
♂♀
+
♂
+
+
BXD40
+
♂♂♀
+
+
+
+
+
BXD42
+
♂♂ ♀
+
+
+
BXD67
+
♀ ♀
+
+
+
+
+
BXD68
+
♀ ♀
+
♂
+
+
+
+
+
+
+
+
+
+
+
+
About the tissue used to generate these data:
+
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 83 arrays were used: 67 were female pools and 16 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).
+
+
+
About data processing:
+
+
Probe set data from the .TXT file: These .TXT files
+were generated using the MAS 5.0.
+
+
Step 1: We added an offset of 1.0 to the .TXT expression values
+for each cell to ensure that all values could be logged without
+generating negative values.
+
Step 2: We took the log base 2 of each cell.
+
Step 3: We computed the Z-score for each cell.
+
Step 4: We multiplied all Z scores by 2.
+
Step 5: We added 8 to the value of all Z-scores. The consequence
+of this simple set of transformations is to produce a set of Z-scores
+that have a mean of 8, a variance of 4, and a standard deviation
+of 2. The advantage of this modified Z-score is that a two-fold
+difference in expression level corresponds approximately to a 1
+unit difference.
+
Step 6: We computed the arithmetic mean of the values for the
+set of microarrays for each of the individual strains.
+
+
Every microarray data set therefore has a mean expression of 8 with
+a standard deviation of 2. A 1-unit difference therefor represents
+roughly a two-fold difference in expression level. Expression levels
+below 5 are usually close to background noise levels.
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 (mm4) Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
+
+
+
+
+
+
+
Strain
+
+
+
+Age
+
+
+
Strain
+
+
+
+Age
+
+
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+
C57BL/6J (B6)
+
♂♂♂
+
♀
+
♀
+
DBA/2J (D2)
+
♀
+
♂♂♀
+
+
+
+
B6D2F1 (F1)
+
♀ ♀
+
♀
+
+
BXD1
+
♀♀
+
+
♀
+
+
+
BXD2
+
♂
+
♀
+
♀
+
BXD5
+
♂♂♀
+
+
+
+
+
BXD6
+
♀
+
+
+
BXD8
+
♀
+
♂♀
+
+
+
+
BXD9
+
♂
+
♀
+
♀
+
BXD11
+
♀♀
+
+
♀
+
+
+
BXD12
+
+
♂
+
♀
+
BXD13
+
♀
+
+
+
+
+
BXD14
+
+
♀♀
+
♀
+
BXD15
+
♀
+
+
♀
+
+
+
BXD16
+
♀
+
♀
+
+
BXD18
+
♀
+
♂
+
♀
+
+
+
BXD19
+
♀
+
♀
+
♀
+
BXD21
+
♀♀
+
♂♂
+
+
+
+
BXD22
+
♀
+
♀♀
+
+
BXD23
+
♀
+
+
+
+
+
BXD24
+
♀♀
+
+
♀
+
BXD25
+
♀♀
+
♀♀
+
+
+
+
BXD27
+
+
+
♀♀
+
BXD28
+
♀
+
♀
+
♀
+
+
+
BXD29
+
♂
+
+
♀
+
BXD31
+
♀♀
+
♀♀
+
+
+
+
BXD32
+
♀
+
♂♀
+
♀
+
BXD33
+
♂♀
+
♀
+
+
+
+
BXD34
+
♂♀
+
♀
+
+
BXD38
+
♂♀♀
+
+
+
+
+
BXD39
+
♂♀
+
♂
+
+
BXD40
+
♂♂♀
+
+
+
+
+
BXD42
+
♂♂ ♀
+
+
+
BXD67
+
♀ ♀
+
+
+
+
+
BXD68
+
♀ ♀
+
♂
+
+
+
+
+
+
+
+
+
+
+
+
About the tissue used to generate these data:
+
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 83 arrays were used: 67 were female pools and 16 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).
+
+
+
About data processing:
+
+
Probe set data from the .TXT file: These .TXT files
+were generated using the PDNN.
+
+
Step 1: We added an offset of 1.0 to the .TXT expression values
+for each cell to ensure that all values could be logged without
+generating negative values.
+
Step 2: We took the log base 2 of each cell.
+
Step 3: We computed the Z-score for each cell.
+
Step 4: We multiplied all Z scores by 2.
+
Step 5: We added 8 to the value of all Z-scores. The consequence
+of this simple set of transformations is to produce a set of Z-scores
+that have a mean of 8, a variance of 4, and a standard deviation
+of 2. The advantage of this modified Z-score is that a two-fold
+difference in expression level corresponds approximately to a 1
+unit difference.
+
Step 6: We computed the arithmetic mean of the values for the
+set of microarrays for each of the individual strains.
+
+
Every microarray data set therefore has a mean expression of 8 with
+a standard deviation of 2. A 1-unit difference therefor represents
+roughly a two-fold difference in expression level. Expression levels
+below 5 are usually close to background noise levels.
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
+
+
+
+
+
+
+
Strain
+
+
+
+Age
+
+
+
Strain
+
+
+
+Age
+
+
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+8 Wks
+
+
+
+
+20 Wks
+
+
+
+
+52 Wks
+
+
+
+
+
C57BL/6J (B6)
+
♂♂♂
+
♀
+
♀
+
DBA/2J (D2)
+
♀
+
♂♂♀
+
+
+
+
B6D2F1 (F1)
+
♀ ♀
+
♀
+
+
BXD1
+
♀♀
+
+
♀
+
+
+
BXD2
+
♂
+
♀
+
♀
+
BXD5
+
♂♂♀
+
+
+
+
+
BXD6
+
♀
+
+
+
BXD8
+
♀
+
♂♀
+
+
+
+
BXD9
+
♂
+
♀
+
♀
+
BXD11
+
♀♀
+
+
♀
+
+
+
BXD12
+
+
♂
+
♀
+
BXD13
+
♀
+
+
+
+
+
BXD14
+
+
♀♀
+
♀
+
BXD15
+
♀
+
+
♀
+
+
+
BXD16
+
♀
+
♀
+
+
BXD18
+
♀
+
♂
+
♀
+
+
+
BXD19
+
♀
+
♀
+
♀
+
BXD21
+
♀♀
+
♂♂
+
+
+
+
BXD22
+
♀
+
♀♀
+
+
BXD23
+
♀
+
+
+
+
+
BXD24
+
♀♀
+
+
♀
+
BXD25
+
♀♀
+
♀♀
+
+
+
+
BXD27
+
+
+
♀♀
+
BXD28
+
♀
+
♀
+
♀
+
+
+
BXD29
+
♂
+
+
♀
+
BXD31
+
♀♀
+
♀♀
+
+
+
+
BXD32
+
♀
+
♂♀
+
♀
+
BXD33
+
♂♀
+
♀
+
+
+
+
BXD34
+
♂♀
+
♀
+
+
BXD38
+
♂♀♀
+
+
+
+
+
BXD39
+
♂♀
+
♂
+
+
BXD40
+
♂♂♀
+
+
+
+
+
BXD42
+
♂♂ ♀
+
+
+
BXD67
+
♀ ♀
+
+
+
+
+
BXD68
+
♀ ♀
+
♂
+
+
+
+
+
+
+
+
+
+
+
+
About the tissue used to generate these data:
+
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 83 arrays were used: 67 were female pools and 16 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).
+
+
+
About data processing:
+
+
Probe set data from the .TXT file: These .TXT files
+were generated using the PDNN.
+
+
Step 1: We added an offset of 1.0 to the .TXT expression values
+for each cell to ensure that all values could be logged without
+generating negative values.
+
Step 2: We took the log base 2 of each cell.
+
Step 3: We computed the Z-score for each cell.
+
Step 4: We multiplied all Z scores by 2.
+
Step 5: We added 8 to the value of all Z-scores. The consequence
+of this simple set of transformations is to produce a set of Z-scores
+that have a mean of 8, a variance of 4, and a standard deviation
+of 2. The advantage of this modified Z-score is that a two-fold
+difference in expression level corresponds approximately to a 1
+unit difference.
+
Step 6: We computed the arithmetic mean of the values for the
+set of microarrays for each of the individual strains.
+
+
Every microarray data set therefore has a mean expression of 8 with
+a standard deviation of 2. A 1-unit difference therefor represents
+roughly a two-fold difference in expression level. Expression levels
+below 5 are usually close to background noise levels.
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
+NEW AND MORE RIGOROUS QUALITY CONTROL. This November 2005 data freeze provides estimate of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 200 brain samples from 32 strains were hybridized in small pools (n=3) to 75 arrays. Data were processed using the PDNN method of Zhang. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 32 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), the B6D2 F1 intercross progeny, and 29 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+
+
+
+
+
+
+
+
+
+
ID
+
tube ID
+
strain
+
age
+
sex
+
scale factor
+
background average
+
present
+
absent
+
marginal
+
AFFX-b-Actin
+
AFFX-Gapdh
+
chip by
+
+
+
1
S172F1
C57BL/6J
197
F
4.258
77.85
0.406
0.566
0.029
1.19
0.78
DP
+
2
S337F1
C57BL/6J
400
F
13.85
48.52
0.307
0.668
0.025
1.21
0.87
DP
+
3
S092F1
C57BL/6J
79
M
4.242
73.54
0.406
0.567
0.027
1.54
0.87
DP
+
4
S092F2
C57BL/6J
79
M
3.397
69.95
0.341
0.636
0.024
1.94
1
TS
+
5
S169F1
DBA/2J
71
F
5.409
82.14
0.374
0.598
0.028
1.64
0.84
DP
+
6
S286F1
DBA/2J
146
F
7.153
58.85
0.38
0.593
0.027
1.34
0.84
DP
+
7
S101F1
DBA/2J
224
M
12.767
73.57
0.464
0.519
0.017
1.77
0.85
DP
+
8
S098F1
DBA/2J
224
M
6.463
73.6
0.443
0.538
0.019
1.76
0.82
DP
+
9
S238F1
B6D2F1
62
F
4.413
66.75
0.4
0.576
0.025
1.26
0.86
DP
+
10
S191F1
B6D2F1
68
F
5.946
79.59
0.366
0.609
0.025
1.54
0.9
DP
+
11
S273F1
B6D2F1
182
F
6.343
56.54
0.389
0.584
0.027
1.68
0.93
DP
+
12
S233F1
BXD1
58
F
5.693
61.85
0.427
0.548
0.025
1.65
0.81
DP
+
13
S280F1
BXD1
396
F
8.435
57.1
0.369
0.601
0.03
1.53
0.94
DP
+
14
S342F1
BXD1
139
F
8.106
52.79
0.377
0.596
0.027
1.33
0.86
DP
+
15
UT701F1
BXD2
142
F
3.502
49.39
0.316
0.661
0.024
1.71
0.82
TS
+
16
S011F1
BXD2
64
M
9.868
111.34
0.356
0.623
0.02
1.65
0.9
DP
+
17
S340F1
BXD2
361
F
8.769
51.87
0.395
0.578
0.027
1.74
0.83
DP
+
18
UT744
BXD5
56
F
2.927
55.02
0.369
0.609
0.021
1.6
0.95
TS
+
19
UT728F1
BXD5
71
M
1.94
60.54
0.355
0.623
0.023
1.46
0.86
TS
+
20
UT746F1
BXD5
71
M
5.451
51.81
0.279
0.701
0.02
1.54
0.78
Ts
+
21
S378F1
BXD6
61
F
11.907
64.64
0.334
0.64
0.026
2.27
1.02
DP
+
22
S167F1
BXD8
72
F
5.004
67.36
0.397
0.576
0.027
1.26
0.78
DP
+
23
S343F1
BXD8
143
F
8.388
108.64
0.223
0.751
0.026
1.44
0.82
DP
+
24
S193F1
BXD9
432
F
4.356
65.64
0.433
0.543
0.024
2.42
1.06
DP
+
25
S270F1
BXD9
173
F
6.365
58.9
0.388
0.584
0.028
1.95
0.97
DP
+
26
S009F1
BXD9
79
M
5.54
108.74
0.419
0.564
0.017
1.49
0.87
DP
+
27
S194F1
BXD11
441
F
5.918
60.19
0.41
0.564
0.026
2.54
1.08
DP
+
28
S234F1
BXD11
51
F
13.033
51.65
0.34
0.631
0.028
1.47
0.84
DP
+
29
UT745F1
BXD11
97
F
3.28
71.75
0.314
0.666
0.021
1.98
1.02
TS
+
30
S281F1
BXD12
413
F
6.338
57.37
0.411
0.563
0.025
1.89
0.94
DP
+
31
S607F1
BXD12
178
M
4.064
104.51
0.357
0.619
0.024
1.73
0.81
DP
+
32
UT748F1
BXD13
86
F
1.67
73.3
0.394
0.585
0.021
1.72
0.96
TS
+
33
S195F1
BXD14
412
F
5.228
63.85
0.398
0.574
0.028
1.82
1.06
DP
+
34
UT705F1
BXD14
190
F
4.838
41.24
0.329
0.651
0.02
1.89
1.76
TS
+
35
UT706F1
BXD14
134
F
9.609
42.32
0.213
0.77
0.017
1.42
1.02
TS
+
36
S382F1
BXD16
354
F
15.561
59.63
0.307
0.667
0.027
2.06
0.98
DP
+
37
S334bF1
BXD18
57
F
13.787
52.44
0.301
0.674
0.025
1.84
0.94
DP
+
38
S362F2
BXD18
376
F
7.121
76.92
0.368
0.606
0.026
1.77
0.88
DP
+
39
S606F1
BXD18
200
M
4.381
57.38
0.427
0.542
0.031
1.56
0.9
DP
+
40
S236F1
BXD19
56
F
4.935
59.44
0.374
0.599
0.026
1.29
0.84
DP
+
41
S271F1
BXD19
163
F
4.705
64.74
0.425
0.546
0.029
1.68
0.84
DP
+
42
UT743F1
BXD21
64
F
2.996
49.56
0.391
0.587
0.022
1.12
0.83
TS
+
43
UT740F1
BXD21
67
F
5.069
49.3
0.288
0.691
0.021
1.82
0.87
TS
+
44
S120F2
BXD21
236
M
4.765
51.11
0.432
0.543
0.025
1.82
0.87
DP
+
45
S170F1
BXD22
176
F
5.278
72.7
0.39
0.582
0.028
1.45
0.8
DP
+
46
S383F1
BXD22
363
F
6.689
53.68
0.403
0.57
0.028
1.94
0.93
DP
+
47
UT815F1
BXD23
88
F
4.964
50.33
0.31
0.669
0.02
1.53
0.75
TS
+
48
S283F1
BXD24
394
F
5.714
52.6
0.421
0.552
0.027
1.66
0.85
DP
+
49
S384F1
BXD25
355
F
4.931
55.46
0.45
0.527
0.024
2
0.91
DP
+
50
S373F1
BXD25
74
F
3.81
55.67
0.472
0.504
0.024
1.49
0.76
DP
+
51
S376F2
BXD25
198
F
9.208
46.29
0.429
0.546
0.025
2.18
0.83
DP
+
52
S532F1
BXD25
90
F
9.489
47.05
0.406
0.567
0.027
1.64
0.84
DP
+
53
S197F1
BXD28
427
F
7.854
57.94
0.365
0.609
0.026
2.42
1.14
DP
+
54
S171F1
BXD28
192
F
15.407
59.24
0.321
0.653
0.026
1.37
0.82
DP
+
55
S381F1
BXD28
46
F
4.924
57.61
0.439
0.535
0.026
1.97
0.93
DP
+
56
S284F1
BXD29
416
F
5.16
54.1
0.447
0.53
0.023
2.61
1.19
DP
+
57
S344F1
BXD31
139
F
7.434
60.53
0.383
0.592
0.026
1.24
0.8
DP
+
58
S198F1
BXD31
98
F
3.634
76.61
0.414
0.558
0.028
1.73
0.97
DP
+
59
S336bF1
BXD31
70
F
15.326
49.99
0.295
0.681
0.024
1.41
0.85
DP
+
60
S534F2
BXD31
262
F
8.057
52.88
0.412
0.561
0.026
1.74
0.9
DP
+
61
S272F1
BXD32
178
F
7.488
76.4
0.34
0.635
0.025
1.69
0.87
DP
+
62
S341F2
BXD32
365
F
7.82
56.4
0.375
0.598
0.027
1.66
0.83
DP
+
63
Z621F1
BXD32
218
M
2.227
54.86
0.467
0.507
0.026
2
1.6
DP
+
64
Z633F1
BXD33
124
F
1.515
75.52
0.469
0.506
0.025
2.21
1.13
DP
+
65
UT704F1
BXD33
184
F
4.242
47.71
0.339
0.642
0.019
2.19
0.97
TS
+
66
Z632F1
BXD33
124
M
2.446
64.45
0.438
0.538
0.024
3.22
1.59
DP
+
67
UT747F1
BXD38
69
F
2.111
61.16
0.404
0.575
0.021
1.67
0.78
TS
+
68
UT780
BXD38
55
F
5.97
47.19
0.297
0.683
0.02
1.45
0.81
TS
+
69
UT749F1
BXD38
69
M
1.15
84.52
0.435
0.544
0.021
1.48
0.82
TS
+
70
S598F1
BXD39
119
F
3.619
117.44
0.308
0.662
0.03
1.56
0.73
DP
+
71
S603-IFI
BXD40
66
M
5.426
83.22
0.381
0.594
0.025
1.42
0.74
DP
+
72
Z640F1
BXD42
109
M
1.935
60.72
0.444
0.529
0.027
1.92
0.96
DP
+
73
UT767F1
BXD67
57
F
1.688
58.3
0.403
0.575
0.022
1.95
0.82
TS
+
74
S536F1
BXD67
79
F
3.886
98.34
0.358
0.616
0.026
1.65
0.92
TS
+
75
UT768F1
BXD68
276
M
2.627
79.2
0.32
0.659
0.02
1.69
1.07
TS
+
+
+
+
+
+
+
How to download these data:
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 75 such pooled samples were arrayed: 58 from females and 17 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 75 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
About data processing:
+
+
Probe set data: The expression data were transformed by Yanhua Qu. The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
+
+
PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
+
+
When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
+
+
+
+
+
About the array probe set names:
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target): Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, December 2003. Updated by YHQ, November, 2005.
+
+This November 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 200 brain samples from 32 strains were hybridized in small pools (n=3) to 75 arrays. Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. The variance of each array has been stabilized to 2 units for easy comparison to other transforms (see below).
+
+
+
+
+
About the cases used to generate this set of data:
+
+
+This data set includes estimate of gene expression for 32 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 29 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current data set (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+
+
+
+
+
+
+
ID
+
tube ID
+
strain
+
age
+
sex
+
scale factor
+
background average
+
present
+
absent
+
marginal
+
AFFX-b-Actin
+
AFFX-Gapdh
+
chip by
+
+
+
1
S172F1
C57BL/6J
197
F
4.258
77.85
0.406
0.566
0.029
1.19
0.78
DP
+
2
S337F1
C57BL/6J
400
F
13.85
48.52
0.307
0.668
0.025
1.21
0.87
DP
+
3
S092F1
C57BL/6J
79
M
4.242
73.54
0.406
0.567
0.027
1.54
0.87
DP
+
4
S092F2
C57BL/6J
79
M
3.397
69.95
0.341
0.636
0.024
1.94
1
TS
+
5
S169F1
DBA/2J
71
F
5.409
82.14
0.374
0.598
0.028
1.64
0.84
DP
+
6
S286F1
DBA/2J
146
F
7.153
58.85
0.38
0.593
0.027
1.34
0.84
DP
+
7
S101F1
DBA/2J
224
M
12.767
73.57
0.464
0.519
0.017
1.77
0.85
DP
+
8
S098F1
DBA/2J
224
M
6.463
73.6
0.443
0.538
0.019
1.76
0.82
DP
+
9
S238F1
B6D2F1
62
F
4.413
66.75
0.4
0.576
0.025
1.26
0.86
DP
+
10
S191F1
B6D2F1
68
F
5.946
79.59
0.366
0.609
0.025
1.54
0.9
DP
+
11
S273F1
B6D2F1
182
F
6.343
56.54
0.389
0.584
0.027
1.68
0.93
DP
+
12
S233F1
BXD1
58
F
5.693
61.85
0.427
0.548
0.025
1.65
0.81
DP
+
13
S280F1
BXD1
396
F
8.435
57.1
0.369
0.601
0.03
1.53
0.94
DP
+
14
S342F1
BXD1
139
F
8.106
52.79
0.377
0.596
0.027
1.33
0.86
DP
+
15
UT701F1
BXD2
142
F
3.502
49.39
0.316
0.661
0.024
1.71
0.82
TS
+
16
S011F1
BXD2
64
M
9.868
111.34
0.356
0.623
0.02
1.65
0.9
DP
+
17
S340F1
BXD2
361
F
8.769
51.87
0.395
0.578
0.027
1.74
0.83
DP
+
18
UT744
BXD5
56
F
2.927
55.02
0.369
0.609
0.021
1.6
0.95
TS
+
19
UT728F1
BXD5
71
M
1.94
60.54
0.355
0.623
0.023
1.46
0.86
TS
+
20
UT746F1
BXD5
71
M
5.451
51.81
0.279
0.701
0.02
1.54
0.78
Ts
+
21
S378F1
BXD6
61
F
11.907
64.64
0.334
0.64
0.026
2.27
1.02
DP
+
22
S167F1
BXD8
72
F
5.004
67.36
0.397
0.576
0.027
1.26
0.78
DP
+
23
S343F1
BXD8
143
F
8.388
108.64
0.223
0.751
0.026
1.44
0.82
DP
+
24
S193F1
BXD9
432
F
4.356
65.64
0.433
0.543
0.024
2.42
1.06
DP
+
25
S270F1
BXD9
173
F
6.365
58.9
0.388
0.584
0.028
1.95
0.97
DP
+
26
S009F1
BXD9
79
M
5.54
108.74
0.419
0.564
0.017
1.49
0.87
DP
+
27
S194F1
BXD11
441
F
5.918
60.19
0.41
0.564
0.026
2.54
1.08
DP
+
28
S234F1
BXD11
51
F
13.033
51.65
0.34
0.631
0.028
1.47
0.84
DP
+
29
UT745F1
BXD11
97
F
3.28
71.75
0.314
0.666
0.021
1.98
1.02
TS
+
30
S281F1
BXD12
413
F
6.338
57.37
0.411
0.563
0.025
1.89
0.94
DP
+
31
S607F1
BXD12
178
M
4.064
104.51
0.357
0.619
0.024
1.73
0.81
DP
+
32
UT748F1
BXD13
86
F
1.67
73.3
0.394
0.585
0.021
1.72
0.96
TS
+
33
S195F1
BXD14
412
F
5.228
63.85
0.398
0.574
0.028
1.82
1.06
DP
+
34
UT705F1
BXD14
190
F
4.838
41.24
0.329
0.651
0.02
1.89
1.76
TS
+
35
UT706F1
BXD14
134
F
9.609
42.32
0.213
0.77
0.017
1.42
1.02
TS
+
36
S382F1
BXD16
354
F
15.561
59.63
0.307
0.667
0.027
2.06
0.98
DP
+
37
S334bF1
BXD18
57
F
13.787
52.44
0.301
0.674
0.025
1.84
0.94
DP
+
38
S362F2
BXD18
376
F
7.121
76.92
0.368
0.606
0.026
1.77
0.88
DP
+
39
S606F1
BXD18
200
M
4.381
57.38
0.427
0.542
0.031
1.56
0.9
DP
+
40
S236F1
BXD19
56
F
4.935
59.44
0.374
0.599
0.026
1.29
0.84
DP
+
41
S271F1
BXD19
163
F
4.705
64.74
0.425
0.546
0.029
1.68
0.84
DP
+
42
UT743F1
BXD21
64
F
2.996
49.56
0.391
0.587
0.022
1.12
0.83
TS
+
43
UT740F1
BXD21
67
F
5.069
49.3
0.288
0.691
0.021
1.82
0.87
TS
+
44
S120F2
BXD21
236
M
4.765
51.11
0.432
0.543
0.025
1.82
0.87
DP
+
45
S170F1
BXD22
176
F
5.278
72.7
0.39
0.582
0.028
1.45
0.8
DP
+
46
S383F1
BXD22
363
F
6.689
53.68
0.403
0.57
0.028
1.94
0.93
DP
+
47
UT815F1
BXD23
88
F
4.964
50.33
0.31
0.669
0.02
1.53
0.75
TS
+
48
S283F1
BXD24
394
F
5.714
52.6
0.421
0.552
0.027
1.66
0.85
DP
+
49
S384F1
BXD25
355
F
4.931
55.46
0.45
0.527
0.024
2
0.91
DP
+
50
S373F1
BXD25
74
F
3.81
55.67
0.472
0.504
0.024
1.49
0.76
DP
+
51
S376F2
BXD25
198
F
9.208
46.29
0.429
0.546
0.025
2.18
0.83
DP
+
52
S532F1
BXD25
90
F
9.489
47.05
0.406
0.567
0.027
1.64
0.84
DP
+
53
S197F1
BXD28
427
F
7.854
57.94
0.365
0.609
0.026
2.42
1.14
DP
+
54
S171F1
BXD28
192
F
15.407
59.24
0.321
0.653
0.026
1.37
0.82
DP
+
55
S381F1
BXD28
46
F
4.924
57.61
0.439
0.535
0.026
1.97
0.93
DP
+
56
S284F1
BXD29
416
F
5.16
54.1
0.447
0.53
0.023
2.61
1.19
DP
+
57
S344F1
BXD31
139
F
7.434
60.53
0.383
0.592
0.026
1.24
0.8
DP
+
58
S198F1
BXD31
98
F
3.634
76.61
0.414
0.558
0.028
1.73
0.97
DP
+
59
S336bF1
BXD31
70
F
15.326
49.99
0.295
0.681
0.024
1.41
0.85
DP
+
60
S534F2
BXD31
262
F
8.057
52.88
0.412
0.561
0.026
1.74
0.9
DP
+
61
S272F1
BXD32
178
F
7.488
76.4
0.34
0.635
0.025
1.69
0.87
DP
+
62
S341F2
BXD32
365
F
7.82
56.4
0.375
0.598
0.027
1.66
0.83
DP
+
63
Z621F1
BXD32
218
M
2.227
54.86
0.467
0.507
0.026
2
1.6
DP
+
64
Z633F1
BXD33
124
F
1.515
75.52
0.469
0.506
0.025
2.21
1.13
DP
+
65
UT704F1
BXD33
184
F
4.242
47.71
0.339
0.642
0.019
2.19
0.97
TS
+
66
Z632F1
BXD33
124
M
2.446
64.45
0.438
0.538
0.024
3.22
1.59
DP
+
67
UT747F1
BXD38
69
F
2.111
61.16
0.404
0.575
0.021
1.67
0.78
TS
+
68
UT780
BXD38
55
F
5.97
47.19
0.297
0.683
0.02
1.45
0.81
TS
+
69
UT749F1
BXD38
69
M
1.15
84.52
0.435
0.544
0.021
1.48
0.82
TS
+
70
S598F1
BXD39
119
F
3.619
117.44
0.308
0.662
0.03
1.56
0.73
DP
+
71
S603-IFI
BXD40
66
M
5.426
83.22
0.381
0.594
0.025
1.42
0.74
DP
+
72
Z640F1
BXD42
109
M
1.935
60.72
0.444
0.529
0.027
1.92
0.96
DP
+
73
UT767F1
BXD67
57
F
1.688
58.3
0.403
0.575
0.022
1.95
0.82
TS
+
74
S536F1
BXD67
79
F
3.886
98.34
0.358
0.616
0.026
1.65
0.92
TS
+
75
UT768F1
BXD68
276
M
2.627
79.2
0.32
0.659
0.02
1.69
1.07
TS
+
+
+
+
+
+
+
About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 75 such pooled samples were arrayed: 58 from females and 17 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 75 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
+
+
+
+
About data processing:
+
+
+Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples.
+
+
This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized variance of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
+
+
+
How to download these data:
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
About the array probe set names:
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target) : Designates a sense target; almost always generated in error.
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
This text file originally generated by RWW, YHQ, and EJC, March 2004. Updated by RWW, November 30, 2005.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be 45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 100 arrays were used: 74 were female pools and 26 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year). you can select the strain symbol in the table above to review some details about the specific cases. You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About data processing:
+
+
Probe set data: The expression values
+were generated using the dChip
+including perfect match data.
+
+
Step 1: We added an offset of 1 to the expression values
+for each cell to ensure that all values could be logged without
+generating negative values.
+
Step 2: We took the log base 2 of each cell.
+
Step 3: We computed the Z-score for each cell.
+
Step 4: We multiplied all Z scores by 2.
+
Step 5: We added 8 to the value of all Z-scores. The consequence
+of this simple set of transformations is to produce a set of Z-scores
+that have a mean of 8, a variance of 4, and a standard deviation
+of 2. The advantage of this modified Z-score is that a two-fold
+difference in expression level corresponds approximately to a 1
+unit difference.
+
Step 6.1: We computed the arithmetic mean of the values for the
+set of microarrays for each of technical duplicate for the individual
+strains.
+
Step 6.2: We computed the arithmetic mean of the values for the
+set of microarrays for each of the individual strains.
+
+
Every microarray data set therefore has a mean expression of 8 with
+a standard deviation of 2. A 1-unit difference therefor represents
+roughly a two-fold difference in expression level. Expression levels
+below 5 are usually close to background noise levels.
+
+
+
Data source acknowledgment:
+
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 100 arrays were used: 74 were female pools and 26 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year). you can select the strain symbol in the table above to review some details about the specific cases. You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About data processing:
+
+
Probe set data: The expression values
+were generated using the dChip
+including perfect match and Missmatch data.
+
+
Step 1: We added an offset of 5000 to the expression values
+for each cell to ensure that all values could be logged without
+generating negative values.
+
Step 2: We took the log base 2 of each cell.
+
Step 3: We computed the Z-score for each cell.
+
Step 4: We multiplied all Z scores by 2.
+
Step 5: We added 8 to the value of all Z-scores. The consequence
+of this simple set of transformations is to produce a set of Z-scores
+that have a mean of 8, a variance of 4, and a standard deviation
+of 2. The advantage of this modified Z-score is that a two-fold
+difference in expression level corresponds approximately to a 1
+unit difference.
+
Step 6.1: We computed the arithmetic mean of the values for the
+set of microarrays for each of technical duplicate for the individual
+strains.
+
Step 6.2: We computed the arithmetic mean of the values for the
+set of microarrays for each of the individual strains.
+
+
Every microarray data set therefore has a mean expression of 8 with
+a standard deviation of 2. A 1-unit difference therefor represents
+roughly a two-fold difference in expression level. Expression levels
+below 5 are usually close to background noise levels.
+
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 (mm4) Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 100 arrays were used: 74 were female pools and 26 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year). you can select the strain symbol in the table above to review some details about the specific cases. You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About data processing:
+
+
Probe set raw data from the .TXT file: These .TXT files
+were generated using the dChip
+including perfect match and Mismatch data.
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 (mm4) Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
+
+All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
+
+
+
The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 100 arrays were used: 74 were female pools and 26 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year). you can select the strain symbol in the table above to review some details about the specific cases. You can also click on the individual symbols (males or females) to view the array image.
+
+
+
About data processing:
+
+
Probe set original data from the .TXT file: These .TXT files
+were generated using the dChip
+including perfect match data.
+
+
About the chromosome and megabase position values:
+
+
The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 (mm4) Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
+
+
About the array probe set names:
+
In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
+
Probe set name designations
+
_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.
+
_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.
+
_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .
+
_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."
+
_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel.
+
+RECOMMENDED BRAIN DATA SET. This December 2003 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 100 arrays. Data were processed using a new method called the Heritability Weighted Transform (HWT) developed by Kenneth F. Manly and Robert W. Williams. Our initial results demonstrate that the HWT1PM transform generates estimates of gene expression that yield more significant QTLs than RMA, dChip, PDNN, or MAS 5.
+
+
+
+
+
About the cases used to generate this set of data:
+
+This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
+
+
BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
+
+
In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
+
+
+
+
+The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
+
+All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.
+
+
+
+
+
+About the samples used to generate these data:
+
+
+Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
+
+
+
+
+About the array platform:
+
+
+Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify UCSC and Verify Emsembllinks in the Trait Data and Editing Form (see buttons to the right side of the Location line).
+
+
+
+
+Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match (PM) probes and 16 mismatch controls (MM). Each set of these probe has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
+
+
f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
+
+
s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
+
+
g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
+
+
r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
+
+
i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
+
+
st (sense target) : Designates a sense target; almost always generated in error.
HWT1PM is an acronym for heritability weighted transform version 1, perfect match probes only.
+
+
Most Affmetrix transforms generate a single consensus estimate of expression based on as many as 32 probes that hybridize with variable selectivity to the target transcript. Each probe could be given an equal weight to derive a consensus estimate of expression (essentially one vote per probe). However, the hybridization performance of probes and their ability to generate a biologically meaningful estimate of mRNA level is highly variable and idiosyncratic; depending on melting temperature, stacking energy, the mixture of background transcripts, and characteristics of reactions used to extract mRNA and to generated labeled cRNA. A simple way to evaluate the performance of probes is to compute their heritabiity within a large data set.
+
+
Heritability is essentially the ratio of genetic variance to the total variance. A highly informative probe is one with little variability within strain but a great deal of variability among strains; essentially the main effect of "strain" in an analysis of variance (ANOVA). Heritability estimated in this way is necessary but not sufficient to define a QTL. To define a QTL, the variation must also correlate with genotypes at some genomic location(s).
+
+We have studied 35 strains and can therefore estimate the "between-strain variance." We have also typically performed three biological replicates within strain. Therefore, we can estimate genetic and non-genetic sources of variance. In our study we have minimized non-genetic variance by pooling samples and by rearing all mice in a standard laboratory environment. We are in a good position to estimate these two variance components and compute the heritability of the 490,000 probes on the U74Av2 array. All of these estimates, both for the perfect match (PM) and mismatch (MM) probes, are provided in the PROBE INFORMATION table associated with every transcript (click on the work "Probe" in any of the TRAIT DATA pages).
+
+
Estimation of Heritability: Individual probe intensities from Affymetrix U74Av2 microarrays were log2-transformed and normalized to a standard array-wide mean of 8 units and a standard deviation of 2 units as described for several other data sets (e.g., UTHSC Brain mRNA U74Av2 (Dec03) MAS5).
+
+
For each probe, the mean squared deviations within strains (MSw) and the mean square deviation between strains (MSb) were calculated by ANOVA. Raw heritability was estimated as (MSb-MSw)/(n x MSt), where n is the average number of replicates per strain (usually 3) and MSt is total variance in the 100 array data set. These particular raw heritability estimates are provided in the PROBE INFORMATION table for each transcript (click on the blue word "Probe" in any of the TRAIT DATA pages and then scroll to the far right column labeled 100brains h2). Note, these raw heritabilities may have negative values because they are calculated from the difference of two estimates subject to sampling error.
+
+
Adjusted heritability was derived from raw heritability by assigning values of 0 and 1, respectively, to raw heritability values below 0.0 or above 1.0. Weights for each probe were calculated by dividing the adjusted heritability by the mean adjusted heritability for all probes in the probeset. In essence this divides the 16 total votes (there are 16 PM probes per probe set) on the basis of their heritability scores. For example. If 8 of the probes had a heritability of 0.5, 4 had a heritability of 0.25, and 4 had a heritability of 0, then these three groups would get weights of 1.6, 0.8, and 0, respectively in generating the consensus estimate of expression level. Expression estimates for each probe set were calculated as the weighted average of those probe-specific means, using the heritability weights just described. The final expression estimates for each strain were calculated as an unweighted average of all biological replicates within each strain.
+
+
+
General Comment: From a statistical point of view the 100 arrays data set we are working with has four dimensions. The first dimension is genetic, and is formed by the set of genetically distinct inbred strains (n = 35) and their genotypes. The second dimension in non-genetic and is represented by the replicate samples within each isogenic line. The third dimension is formed by the multiple probes that make up each probe set. There are up to 32 probes per probe set, but in this transform we have focused attention only on the 16 PM probes. Finally, the fourth dimension is represented by the 12422 probe sets that target different transcripts. For genetic analysis and QTL mapping, dimensions 2 and 3 must be collapsed into single estimate of mean gene expression for each strain that can be compared with genotypes (dimension 1). Heritability is determined by the relative expression variance contributed by dimensions 1 and 2. The HWT1PM method uses the information from dimensions 1 and 2 to define weights that allow dimension 3 to be collapsed using a weighted average. Dimension 2 is still collapsed using a simple average.
+
+
+
+
+
+Data source acknowledgment:
+
Data were generated with funds to RWW from the Dunavant Chair of
+Excellence, University of Tennessee Health Science Center, Department
+of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
+
+
+
Information about this text file:
+
+This text file originally generated by RWW and KFM, December 2003. Updated by RWW, Oct 31, Nov 6, 2004 and by KFM Nov 8, 2004.
+
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+
+
+
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+ 
+ 
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+ 
