UNC Agilent G4121A Liver Database (Jan06 Freeze) Orig LOWESS modify this page

Accession number: GN105

    Summary:

FINAL DATA FREEZE: This data set provides estimates of mRNA expression in livers of 43 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, Daniel Gatti, 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).

    About the cases used to generate this set of data:

Ninety-six BXD and parental strain 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. Forty mouse strains were used. Thirty-seven strains are 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
M and F
BXD2
BXD5
M and F
BXD5
BXD6
M and F
BXD6
BXD8
M and F
BXD8
BXD9
M and F
BXD9
BXD11
M and F
BXD11
BXD12
M and F
BXD12
BXD13
M and F
BXD13
BXD14
M and F
BXD14
BXD15
M and F
BXD15
BXD21
M and F
BXD21
BXD23
F
BXD23
BXD24
M
BXD24
BXD28
M and F
BXD28
BXD29
M and F
BXD29
BXD31
M and F
BXD31
BXD32
M and F
BXD32
BXD33
F
BXD33
BXD34
M and F
BXD34
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
M and F
BXD45
BXD48
M and F
BXD48
BXD51
M and F
BXD51
BXD60
M and F
BXD60
BXD62
M and F
BXD62
BXD69
M and F
BXD69
BXD73
M and F
BXD73
BXD77
M and F
BXD77
BXD85
M and F
BXD85
BXD86
M and F
BXD86
BXD92
M and F
BXD92
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
35783
DBA/2J F B1
1
1
DBA/2J
F
251197818090
3
35782
C57BL/6J F B1
1
5
C57BL/6J
F
251197818089
3
35770
BXD1 M
1
9
BXD1
M
251197817936
3
35771
BXD12 F
1
13
BXD12
F
251197817937
3
35772
BXD23 M
1
24
BXD14
M
251197817938
3
35774
BXD28 M
1
29
BXD28
M
251197817940
3
35775
BXD29 F
1
30
BXD29
F
251197817941
3
35773
BXD34 F
1
43
BXD34
F
251197817939
3
35776
BXD39 M
1
54
BXD39
M
251197817942
3
35777
BXD40 F
1
59
BXD40
F
251197817943
2
35778
BXD77 M
1
500
BXD77
M
251197817959
2
35768
B6D2F1 M B1
1
609
B6D2F1
M
251197817934
3
35779
BXD8 F
1
613
BXD8
F
251197817960
3
35781
C57BL/6J M B1
1
614
C57BL/6J
M
251197818088
2
35780
C57BL/6J M B1R
1
614
C57BL/6J
M
251197817961
2
35535
DBA/2J F B2
2
1
DBA/2J
F
251197818160
3
35537
DBA/2J F B2(3)
2
3
DBA/2J
F
251197818162
3
35536
DBA/2J M B2
2
4
DBA/2J
M
251197818161
3
35941
C57BL/6J F
2
5
C57BL/6J
F
251197818159
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
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
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
BXD62 M
2
79
BXD62
M
251197817948
3
35531
BXD43 F
2
81
BXD43
F
251197818085
3
35539
B6D2F1 F
2
601
B6D2F1
F
251197818177
3
35528
B6D2F1 M
2
603
B6D2F1
M
251197818084
3
35919
DBA/2J F B3
3
1
DBA/2J
F
251197817968
3
35918
C57BL/6J F B3
3
5
C57BL/6J
F
251197817967
3
35923
BXD14 M
3
17
BXD14
M
251197817972
3
35924
BXD15 F
3
19
BXD15
F
251197817973
3
35938
BXD36M
3
46
BXD36
M
16011978011758
3
35937
BXD38F
3
52
BXD38
F
16011978011757
3
35939
BXD6 M
3
69
BXD6
M
16011978011759
3
35936
BXD9F
3
70
BXD9
F
16011978011756
3
35930
BXD60 M
3
86
BXD60
M
16011978011860
2
35931
BXD44 F
3
87
BXD44
F
16011978011861
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
35921
B6D2F1 F B3
3
602
B6D2F1
F
251197817970
3
35920
C57BL/6J F B3(605)
3
605
C57BL/6J
F
251197817969
3
35922
B6D2F1 M B3
3
702
B6D2F1
M
251197817971
3
39357
B4R DBA/2J F
4R
1
DBA/2J
F
251197826041
3
39356
B4R C57BL/6J F B4
4R
5
C57BL/6J
F
251197826040
3
39383
B4R C57BL/6J F B4R
4R
5
C57BL/6J
F
251197826108
3
39352
B4R BXD24 F
4R
25
BXD24
M
251197826026
2
39355
B4R BXD40 M
4R
60
BXD40
M
251197826029
3
39361
B4R BXD51 M
4R
77
BXD51
M
251197826105
3
39360
B4R DBA/2J F (607)
4R
607
DBA/2J
F
251197826043
3
39354
B4R BXD32 M
4R
701
BXD32
M
251197826028
3
39351
B4R BXD23 F
4R
704
BXD14
F
251197826025
3
39359
B4R BXD16 M
4R
803
BXD16
M
251197826044
3
39353
B4R BXD19 F
4R
804
BXD19
F
251197826027
3
39381
B4R BXD62 F
4R
812
BXD62
F
251197826106
3
39348
B4R BXD69 F
4R
813
BXD69
F
251197825672
3
39349
B4R BXD73 M
4R
816
BXD73
M
251197825673
3
39347
B4R BXD8 M
4R
817
BXD8
M
251197825670
3
39382
B4R BXD85 F
4R
818
BXD85
F
251197826107
3
39346
B4R BXD86 F
4R
819
BXD86
F
251197825669
3
39350
B4R BXD92 F
4R
821
BXD92
F
251197825674
3
39358
B4R C57BL/6J F B4(823)
4R
823
C57BL/6J
F
251197826042
3
35550
DBA/2J F B5
5
1
DBA/2J
F
251197817950
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
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
35553
BXD60 F
5
84
BXD60
F
251197818019
3
35585
BXD77 F
5
499
BXD77
F
251197818037
3
35555
BXD45 F
5
515
BXD45
F
251197818021
2
35787
DBA/2J F B6
6
1
DBA/2J
F
251197818005
3
35786
C57BL/6J F B6
6
5
C57BL/6J
F
251197818004
3
35800
C57BL/6J F B6R
6
5
C57BL/6J
F
251197818123
3
35795
BXD21 F
6
20
BXD21
F
251197818114
3
35791
BXD24 M
6
26
BXD24
M
251197818115
3
35794
BXD31 F
6
32
BXD31
F
251197818118
2
35792
BXD33 F
6
40
BXD33
F
251197818116
3
35790
BXD34 M
6
42
BXD34
M
251197818008
3
35793
BXD9 M
6
71
BXD9
M
251197818117
3
35797
BXD44 M
6
502
BXD44
M
251197818120
2
35788
C57BL/6J M B6(507)
6
507
C57BL/6J
M
251197818006
2
35789
DBA/2J M B6(510)
6
510
DBA/2J
M
251197818007
2
35798
BXD48 M
6
512
BXD48
M
251197818121
2
35796
BXD2 F
6
612
BXD2
F
251197818119
3
35567
DBA/2J F B7
7
1
DBA/2J
F
251197818069
3
35566
C57BL/6J F B7
7
5
C57BL/6J
F
251197818023
3
35577
C57BL/6J F B7R
7
5
C57BL/6J
F
251197818156
3
35568
BXD29 M
7
31
BXD29
M
251197818071
3
35570
BXD38 M
7
51
BXD38
M
251197818073
3
35573
BXD42 F
7
62
BXD42
F
251197818126
3
35574
BXD5 M
7
66
BXD5
M
251197818127
3
35940
BXD6 F
7
68
BXD6
F
251197818128
3
35508
BXD43 M
7
82
BXD43
M
251197818157
2
35575
DBA/2J M B7
7
511
DBA/2J
M
251197818070
2
38670
DBA/2J F B8-02 (1)
8
1
DBA/2J
F
251197828123
3
38669
C57BL/6J F
8
5
C57BL/6J
F
251197828122
3
38668
C57BL/6J F
8
5
C57BL/6J
F
251197828099
3
38697
BXD36 F R
8
48
BXD36
F
251197828218
3
38698
BXD39 F R
8
56
BXD39
F
251197828219
3
38661
BXD48 F
8
92
BXD48
F
251197828096
3
38673
BXD14 F
8
610
BXD23
F
251197828126
3
38686
BXD2 M
8
611
BXD2
M
251197828134
3
38672
BXD11/TY F
8
703
BXD11/TY
F
251197828125
3
38671
B6D2F1 F
8
801
B6D2F1
F
251197828124
3
38694
BXD16 F
8
802
BXD16
F
251197828215
3
38696
BXD19 M
8
805
BXD19
M
251197828217
2
38695
BXD33 F
8
809
BXD33
F
251197828216
3
38667
BXD45 M
8
811
BXD45
M
251197828098
3
38687
BXD69 M
8
814
BXD69
M
251197828135
3
38688
BXD73 F
8
815
BXD73
F
251197828136
2
38689
BXD92 M
8
822
BXD92
M
251197828146
3
38685
BXD86 M
8
901
BXD86
M
251197828133
3
38660
BXD51 F
8
902
BXD51
F
251197828092
3
38666
BXD85 M
8
903
BXD85
M
251197828097
3

Error-Checking Note: The strains of pooled samples were verified by Daniel Gatti and Rob Williams by comparing the genotype on the arrays with the known genotype for each strain. Sample 17 (BXD14M) did not match any other strain. This sample was removed from the dataset. Sample 610 (BXD14F) was found to match the BXD23F genotype and was reassigned. Samples 24 and 704 (BXD23M & F) matched the BXD14 genotype and were reassigned as BXD14 mice. Samples 46 and 48 were found to be of mixed genotype and were removed from the dataset.

The sexes of each pooled sample were checked by Daniel Gatti using Y chromosome expression. Sample 25 (BXD24F) was found to be male. This change was made and there are two BXD24 male samples. Samples 40 and 809 (BXD33) were both found to be female.

    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). In this particular data set, values range from an extreme low of approximately -8 to a high of approximately +4. Of the full set of 20868 probes, a total of 1507 probes (or 7.2%) have a value greater than +1.0; 3651 (17.5%) have a value greater than 0.5; and 10821 (51.9%) have a value of greater than 1.0. It is possible for any user to recompute these type of counts and percentages using the "mean=(low_value, high_value)" command (for example, "mean=(1 5)" will provide a count of all probes with values between 1 and 5).

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

    Citation:

The first manuscript from this work is in press:

Gatti D, Maki A, Chesler EJ, Kosyk O, Kirova R, Lu L, Manly KF, Qu Y, Williams RW, Perkins A, Langston ME, Threadgill DW, Rusyn I (2007) Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology, in press

    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. Updated by DMG, Jan. 5, 2006; RWW, April 17, 2007.