UTHSC Brain mRNA U74Av2 (Nov05) PDNN modify this page

Accession number: GN95

    Summary:

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
1S172F1C57BL/6J197F4.258
77.85
0.4060.5660.0291.190.78DP
2S337F1C57BL/6J400F13.85
48.52
0.3070.6680.0251.210.87DP
3S092F1C57BL/6J79M4.242
73.54
0.4060.5670.0271.540.87DP
4S092F2C57BL/6J79M3.397
69.95
0.3410.6360.0241.941TS
5S169F1DBA/2J71F5.409
82.14
0.3740.5980.0281.640.84DP
6S286F1DBA/2J146F7.153
58.85
0.380.5930.0271.340.84DP
7S101F1DBA/2J224M12.767
73.57
0.4640.5190.0171.770.85DP
8S098F1DBA/2J224M6.463
73.6
0.4430.5380.0191.760.82DP
9S238F1B6D2F162F4.413
66.75
0.40.5760.0251.260.86DP
10S191F1B6D2F168F5.946
79.59
0.3660.6090.0251.540.9DP
11S273F1B6D2F1182F6.343
56.54
0.3890.5840.0271.680.93DP
12S233F1BXD158F5.693
61.85
0.4270.5480.0251.650.81DP
13S280F1BXD1396F8.435
57.1
0.3690.6010.031.530.94DP
14S342F1BXD1139F8.106
52.79
0.3770.5960.0271.330.86DP
15UT701F1BXD2142F3.502
49.39
0.3160.6610.0241.710.82TS
16S011F1BXD264M9.868
111.34
0.3560.6230.021.650.9DP
17S340F1BXD2361F8.769
51.87
0.3950.5780.0271.740.83DP
18UT744BXD556F2.927
55.02
0.3690.6090.0211.60.95TS
19UT728F1BXD571M1.94
60.54
0.3550.6230.0231.460.86TS
20UT746F1BXD5 71M5.451
51.81
0.2790.7010.021.540.78Ts
21S378F1BXD661F11.907
64.64
0.3340.640.0262.271.02DP
22S167F1BXD872F5.004
67.36
0.3970.5760.0271.260.78DP
23S343F1BXD8143F8.388
108.64
0.2230.7510.0261.440.82DP
24S193F1BXD9432F4.356
65.64
0.4330.5430.0242.421.06DP
25S270F1BXD9173F6.365
58.9
0.3880.5840.0281.950.97DP
26S009F1BXD979M5.54
108.74
0.4190.5640.0171.490.87DP
27S194F1BXD11441F5.918
60.19
0.410.5640.0262.541.08DP
28S234F1BXD1151F13.033
51.65
0.340.6310.0281.470.84DP
29UT745F1BXD1197F3.28
71.75
0.3140.6660.0211.981.02TS
30S281F1BXD12413F6.338
57.37
0.4110.5630.0251.890.94DP
31S607F1BXD12178M4.064
104.51
0.3570.6190.0241.730.81DP
32UT748F1BXD1386F1.67
73.3
0.3940.5850.0211.720.96TS
33S195F1BXD14412F5.228
63.85
0.3980.5740.0281.821.06DP
34UT705F1BXD14190F4.838
41.24
0.3290.6510.021.891.76TS
35UT706F1BXD14134F9.609
42.32
0.2130.770.0171.421.02TS
36S382F1BXD16354F15.561
59.63
0.3070.6670.0272.060.98DP
37S334bF1BXD1857F13.787
52.44
0.3010.6740.0251.840.94DP
38S362F2BXD18376F7.121
76.92
0.3680.6060.0261.770.88DP
39S606F1BXD18200M4.381
57.38
0.4270.5420.0311.560.9DP
40S236F1BXD1956F4.935
59.44
0.3740.5990.0261.290.84DP
41S271F1BXD19163F4.705
64.74
0.4250.5460.0291.680.84DP
42UT743F1BXD2164F2.996
49.56
0.3910.5870.0221.120.83TS
43UT740F1BXD21 67F5.069
49.3
0.2880.6910.0211.820.87TS
44S120F2BXD21236M4.765
51.11
0.4320.5430.0251.820.87DP
45S170F1BXD22176F5.278
72.7
0.390.5820.0281.450.8DP
46S383F1BXD22363F6.689
53.68
0.4030.570.0281.940.93DP
47UT815F1BXD2388F4.964
50.33
0.310.6690.021.530.75TS
48S283F1BXD24394F5.714
52.6
0.4210.5520.0271.660.85DP
49S384F1BXD25355F4.931
55.46
0.450.5270.02420.91DP
50S373F1BXD2574F3.81
55.67
0.4720.5040.0241.490.76DP
51S376F2BXD25198F9.208
46.29
0.4290.5460.0252.180.83DP
52S532F1BXD2590F9.489
47.05
0.4060.5670.0271.640.84DP
53S197F1BXD28427F7.854
57.94
0.3650.6090.0262.421.14DP
54S171F1BXD28192F15.407
59.24
0.3210.6530.0261.370.82DP
55S381F1BXD2846F4.924
57.61
0.4390.5350.0261.970.93DP
56S284F1BXD29416F5.16
54.1
0.4470.530.0232.611.19DP
57S344F1BXD31139F7.434
60.53
0.3830.5920.0261.240.8DP
58S198F1BXD3198F3.634
76.61
0.4140.5580.0281.730.97DP
59S336bF1BXD3170F15.326
49.99
0.2950.6810.0241.410.85DP
60S534F2BXD31262F8.057
52.88
0.4120.5610.0261.740.9DP
61S272F1BXD32178F7.488
76.4
0.340.6350.0251.690.87DP
62S341F2BXD32365F7.82
56.4
0.3750.5980.0271.660.83DP
63Z621F1BXD32218M2.227
54.86
0.4670.5070.02621.6DP
64Z633F1BXD33124F1.515
75.52
0.4690.5060.0252.211.13DP
65UT704F1BXD33184F4.242
47.71
0.3390.6420.0192.190.97TS
66Z632F1BXD33124M2.446
64.45
0.4380.5380.0243.221.59DP
67UT747F1BXD3869F2.111
61.16
0.4040.5750.0211.670.78TS
68UT780BXD38 55F5.97
47.19
0.2970.6830.021.450.81TS
69UT749F1BXD3869M1.15
84.52
0.4350.5440.0211.480.82TS
70S598F1BXD39119F3.619
117.44
0.3080.6620.031.560.73DP
71S603-IFIBXD4066M5.426
83.22
0.3810.5940.0251.420.74DP
72Z640F1BXD42109M1.935
60.72
0.4440.5290.0271.920.96DP
73UT767F1BXD6757F1.688
58.3
0.4030.5750.0221.950.82TS
74S536F1BXD6779F3.886
98.34
0.3580.6160.0261.650.92TS
75UT768F1BXD68276M2.627
79.2
0.320.6590.021.691.07TS

    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.
  • Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.

        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, December 2003. Updated by YHQ, November, 2005.