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
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-
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-
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-
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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
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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.
-
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ARNIS: Please revise and update this text. I copied the April 2006 data and have NOT made any modifications below.
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About the lines used to generate this set of data:
-
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-
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.
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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):
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Grain yield (MT/ha)
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Lodging (%)
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Height (cm)
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Heading date (days after January 1)
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Grain protein (%)
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Alpha amylase (20 Deg units)
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Diastatic power (Deg)
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Malt extract (%)
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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 #
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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).
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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.
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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.
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RNA Sample Processing:
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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).
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Replication and Sample Balance:
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Experimental Design and Batch Structure:
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Downloading all data:
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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.
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About the array platform:
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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.
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About data processing:
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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.
-
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Data source acknowledgment:
-
-
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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
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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.
-
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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.
-
-
-
- 
- 
- 
