UNC Agilent G4121A Liver Database (Jul04 Freeze) Orig LOWESS modify this page

    Summary:

This data set provides estimates of mRNA expression in livers of 38 adult BXD recombinant inbred mice measured using Agilent G4121A microarray. Data were generated by a consortium of investigators at the University of North Carolina at Chapel Hill (Akira Maki, David Threadgill, and Ivan Rusyn) and at the University of Tennessee Heath Science Center (Lu Lu, Elissa Chesler, Ken Manly, and Rob Williams). Image intensity data were processed using a locally weighted scatterplot smooth (LOWESS) and are presented without further modification (Orig LOWESS; see section below on Data Processing). For background on the NIEHS Toxicogenomics Research Consortium and the Chemical Effects in Biological Systems (CEBS) program please link to a PDF by Michael D. Waters. This is the first data freeze. This data set is still private. Please contact Dr. Ivan Rusyn for access.

    About the cases used to generate this set of data:

Ninety-six BXD liver sample pools were obtained from animals reared at UTHSC in a pathogen-free vivarium. Mice were experimentally naive and housed at weaning (20 to 24 days-of-age) in same-sex groups in standard mouse shoebox cages. Mice were 56 to 177 days old at the time of sacrifice. Thirty-eight mouse strains were used of which 27 were represented by both sexes.
Strain Name
Sex
WebQTL Strain ID
C57BL/6J
M and F
C57BL/6J
DBA/2J
M and F
DBA/2J
B6D2F1
M and F
F1
BXD1
M and F
BXD1
BXD2
F
BXD2
BXD5
M and F
BXD5
BXD6
M and F
BXD6
BXD8
F
BXD8
BXD9
M and F
BXD9
BXD11
M
BXD11
BXD12
M and F
BXD12
BXD13
M and F
BXD13
BXD14
M
BXD14
BXD15
M and F
BXD15
BXD21
M and F
BXD21
BXD23
M
BXD23
BXD24
M and F
BXD24
BXD28
M and F
BXD28
BXD29
M and F
BXD29
BXD31
M and F
BXD31
BXD32
F
BXD32
BXD33
F (?)
BXD33
BXD34
M and F
BXD34
BXD36
M and F (?)
BXD36
BXD38
M and F
BXD38
BXD39
M and F
BXD39
BXD40
M and F
BXD40
BXD42
M and F
BXD42
BXD43
M and F
BXD43
BXD44
M and F
BXD44
BXD45
F
BXD45
BXD48
M
BXD48
BXD51
F (?)
BXD51
BXD60
M and F
BXD60
BXD62
M and F (?)
BXD62
BXD77
M and F
BXD77
BXD85
M and F (?)
BXD85
BXD86
F (?)
BXD86
C57BL/6J, DBA/2J, and BXD1 through BXD42 were originally obtained from The Jackson Laboratory. Advanced intercross BXD strains (BXD43 and higher) were generated at Princeton University and UTHSC (Peirce and Lu, 2004). All of these new strains were inbred for at least 14 generations.

    About the tissue used to generate these data:

Animals were killed by cervical dislocation. The entire liver was removed within less than 5 minutes by Zhiping Jia or Hongtao Zhai and placed in RNAlater (Ambion) overnight at 4 degrees C. Tissue was stored in single vials (2 to 3 cases per vial) at -80 degrees C. Tissue vials were shipped to UNC on ice by FedEX. Prior to isolation of RNA, liver samples from the same strain and sex (2 to 3 animals) were pooled in equal amount and minced in a homogenization buffer using an electric homogenizer. Total RNA was isolated using Qiagen RNeasy Mini kits according to the manufacturer's instructions. RNA purity and quality were verified using a BioAnalyzer 2100 and Low RNA Input Linear Amplification kits (Agilent Technologies, Wilmington, DE) in these experiments. RNA labeling, array hybridization and washing and other procedures were performed according to the manufacturer's protocols. A common reference design was used. Male C57BL/6J mouse pooled (equal amounts of RNA from liver, kidney, lung, brain and spleen) RNA provided by the Toxicogenomics Research Consortium was used as a common reference in all these experiments.

    About the array platform

Samples were assayed using G4121A Agilent oligomer microarray glass slides ( GEO Platform ID GPL891). This microarray estimate expression of approximately 20,842 mouse genes, including a special set of toxicology transcripts nominated by a collaboration that included the National Institute of Environmental Health Sciences (NIEHS) and members of the Toxicogenomics Research Consortium.
Experiment ID
Experiment Name
Batch#
Sample ID
Strain
Sex
Array Barcode#
Pool Size
35781
C57BL/6J M B1
1
614
C57BL/6J
M
251197818088
2
35780
C57BL/6J M B1R
1
614
C57BL/6J
M
251197817961
2
35782
C57BL/6J F B1
1
5
C57BL/6J
F
251197818089
3
35783
DBA/2J F B1
1
1
DBA/2J
F
251197818090
3
35768
B6D2F1 M B1
1
609
B6D2F1
M
251197817934
3
35769
B6D2F1 F B1
1
96
B6D2F1
Unknown
251197817935
2
35770
BXD1 M
1
9
BXD1
M
251197817936
3
35771
BXD12 F
1
13
BXD12
F
251197817937
3
35772
BXD23 M
1
24
BXD23
M
251197817938
3
35773
BXD34 F
1
43
BXD34
F
251197817939
3
35774
BXD28 M
1
29
BXD28
M
251197817940
3
35775
BXD29 F
1
30
BXD29
F
251197817941
3
35776
BXD39 M
1
54
BXD39
M
251197817942
3
35777
BXD40 F
1
59
BXD40
F
251197817943
2
35778
BXDA10 M
1
500
BXD77
M
251197817959
2
35779
BXD8 F
1
613
BXD8
F
251197817960
3
35509
C57BL/6J M B2
2
8
C57BL/6J
M
251197818158
3
35529
C57BL/6J M B2R
2
8
C57BL/6J
M
251197818086
3
35578
C57BL/6J F B2
2
5
C57BL/6J
F
251197818159
3
35535
DBA/2J F B2
2
1
DBA/2J
F
251197818160
3
35536
DBA/2J M B2
2
4
DBA/2J
M
251197818161
3
35537
DBA/2J F B2(3)
2
3
DBA/2J
F
251197818162
3
35538
C57BL/6J F B2(7)
2
7
C57BL/6J
2F, 1M
251197818163
3
35528
B6D2F1 M
2
603
B6D2F1
M
251197818084
3
35539
B6D2F1 F
2
601
B6D2F1
F
251197818177
3
35540
BXD11 M
2
12
BXD11
M
251197818178
2
35541
BXD13 F
2
16
BXD13
F
251197818179
3
35542
BXD21 M
2
21
BXD21
M
251197818180
3
35543
BXD24 F
2
25
BXD24
F
251197818181
2
35514
BXD31 M
2
34
BXD31
M
251197817944
2
35515
BXD32 F
2
36
BXD32
F
251197817945
2
35516
BXD42 M
2
63
BXD42
M
251197817946
3
35517
BXD5 F
2
65
BXD5
F
251197817947
2
35527
BXDAP15 M
2
79
BXD62
M
251197817948
3
35531
BXDAP19 F
2
81
BXD43
F
251197818085
3
35916
C57BL/6J M B3
3
506
C57BL/6J
M
251197817964
2
35932
C57BL/6J M B3R
3
506
C57BL/6J
M
16011978011862
2
35917
DBA/2J M B3
3
509
DBA/2J
M
251197817966
2
35918
C57BL/6J F B3
3
5
C57BL/6J
F
251197817967
3
35919
DBA/2J F B3
3
1
DBA/2J
F
251197817968
3
35920
C57BL/6J F B3(605)
3
605
C57BL/6J
F
251197817969
3
35921
B6D2F1 F B3
3
602
B6D2F1
F
251197817970
3
35922
B6D2F1 M B3
3
702
B6D2F1
M
251197817971
3
35923
BXD14 M
3
17
BXD14
M
251197817972
3
35924
BXD15 F
3
19
BXD15
F
251197817973
3
35933
BXD33 M
3
39
BXD33
F or M
251197818091
3
35925
BXD9 F
3
70
BXD9
F
16011978011756
3
35926
BXD38 F
3
52
BXD38
F
16011978011757
3
35927
BXD36 M
3
46
BXD36
M
16011978011758
3
35928
BXD6 M
3
69
BXD6
M
16011978011759
3
35929
BXDA23F14 F
3
73
BXD86
F or M
16011978011760
3
35930
BXDAP5F21 M
3
86
BXD60
M
16011978011860
2
35931
BXDAP6F16 F
3
87
BXD44
F
16011978011861
3
35549
C57BL/6J F B5
5
5
C57BL/6J
F
251197817949
3
35587
C57BL/6J F B5R
5
5
C57BL/6J
F
251197818022
3
35550
DBA/2J F B5
5
1
DBA/2J
F
251197817950
3
35558
BXD1 F
5
11
BXD1
F
251197818036
2
35551
BXD12 M
5
14
BXD12
M
251197817952
3
35552
BXD13 M
5
15
BXD13
M
251197817953
2
35584
BXD15 M
5
18
BXD15
M
251197818034
3
35557
BXD28 F
5
28
BXD28
F
251197818035
3
35585
BXDA10 F
5
499
BXD77
F
251197818037
3
35586
BXDAP11 M
5
76
BXD51
M or F
251197818038
3
35553
BXDAP5 F
5
84
BXD60
F
251197818019
3
35554
BXDA22 M
5
513
BXD85
F
251197818020
2
35555
BXDAP12 F
5
515
BXD45
F
251197818021
2
35786
C57BL/6J F B6
6
5
C57BL/6J
F
251197818004
3
35800
C57BL/6J F B6R
6
5
C57BL/6J
F
251197818005
3
35787
DBA/2J F B6
6
1
DBA/2J
F
251197818006
3
35788
C57BL/6J M B6(507)
6
507
C57BL/6J
M
251197818007
2
35789
DBA/2J M B6(510)
6
510
DBA/2J
M
251197818008
2
35790
BXD34 M
6
42
BXD34
M
251197818114
3
35795
BXD21 F
6
20
BXD21
F
251197818115
3
35791
BXD24 M
6
26
BXD24
M
251197818116
3
35792
BXD33 F
6
40
BXD33
F
251197818117
3
35793
BXD9 M
6
71
BXD9
M
251197818118
3
35794
BXD31 F
6
32
BXD31
F
251197818119
2
35796
BXD2 F
6
612
BXD2
F
251197818120
3
35797
BXDAP6F16 M
6
502
BXD44
M
251197818121
2
35798
BXDAP8F21 M
6
512
BXD48
M
251197818122
2
35799
BXDA22F14 M
6
514
BXD85
M or F
251197818123
2
35566
C57BL/6J F B7
7
5
C57BL/6J
F
251197818023
3
35577
C57BL/6J F B7R
7
5
C57BL/6J
F
251197818156
3
35567
DBA/2J F B7
7
1
DBA/2J
F
251197818069
3
35575
DBA/2J M B7
7
511
DBA/2J
M
251197818070
2
35568
BXD29 M
7
31
BXD29
M
251197818071
3
35569
BXD36 F
7
47
BXD36
F or M
251197818072
3
35570
BXD38 M
7
51
BXD38
M
251197818073
3
35571
BXD39 F
7
56
BXD39
F
251197818124
3
35572
BXD40 M
7
60
BXD40
M
251197818125
3
35573
BXD42 F
7
62
BXD42
F
251197818126
3
35574
BXD5 M
7
66
BXD5
M
251197818127
3
35579
BXD6 F
7
68
BXD6
F
251197818128
3
35576
BXDAP15 F
7
78
BXD62
F or M
251197818155
3
35508
BXDAP19 M
7
82
BXD43
M
251197818157
2

Error Checking Note: Sexes of all individual animals used in this analysis were rechecked by Jing Gu and Lu Lu after processing was complete by genotyping Y chromosome-specific microsatellite markers. Sample 7 (also known as Experiment ID 35538) was shown to consist of a pool of two female samples and one male sample. This is the only mixed-sex sample in this study. Sample 513 is a female based both on regenotyping and on the array results. To use the array data to sex an animal we have relied on sex-specific expression differences of gene transcripts. Ddx3y and Uty are good male Y chromosome expression markers, whereas AI314753 and Eif2s3x are good female expression markers. Samples 39, 76, and 514 are males based on laboratory records and based on regenotyping the Y chromosome, but appear to be females based on the "sex" of the array data. Conversely, sample 47, 73, and 78 should be females based on our records and regenotyping, but appear to be males based on array data. We have marked these uncertain cases as M or F in the table.

    About data processing:

Expression data were initially expressed as the ratio of the liver fluorescence signal to that generated by the reference mRNA sample (liver, kidney, lung, brain, and spleen) for each probe. Data were normalized using a robust LOWESS smoothing method that adjusts for non-linearity of signal in the two channels. We then computed the log base 2 of these ratios (median). A value of -1 indicates that expression in liver is roughly 1/2 that in the control; a value of -2 indicates that expression in the liver is roughly 1/4 that in the control, etc. Conversely, a value of +2 indicates that the expression in liver is 4-fold greater in liver.

    About the chromosome and megabase position values:

The chromosomal locations of probes were determined by NCBI's megablast using the NCBI M32 genomic sequence. Gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/ ). We thank Kenneth Phillips (Paradigm Genetics, Inc) for helping generate the probes position data set.

    Data source acknowledgment:

This project was supported by ES10126, ES11391, ES11660 and P20-MH 62009 to KFM and RW. Ivan Rusyn was a recipient of a Transition to Independent Position Award (ES11660) from the National Institute of Environmental Health Sciences. Work by Paradigm Genetics, Inc. in design of the Toxicogenomics Micro (G4121A) array was supported by NIEHS contract N01-ES-25497.
Please contact either:
Ivan Rusyn at the Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431, USA or
Rob Williams at the Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN 38163, USA

    About this text file:

This text file originally generated by Ivan Rusyn, David W. Threadgill and Robert W. Williams, July 2004. Updated by RWW, Nov 14, 16, 2004. Updated by IR, Dec 1, 2004; by RWW June 15, 2005.