UNC Agilent G4121A Liver Database (Jul04 Freeze) Orig LOWESS

    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.

    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. Tissue was stored in single vials (2 to 3 cases per vial) at -80 degrees. 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 (1" x 3" format). 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# 35781 C57BL/6J M B1 1 614 C57BL/6J M 251197818088 35780 C57BL/6J M B1R 1 614 C57BL/6J M 251197817961 35782 C57BL/6J F B1 1 5 C57BL/6J F 251197818089 35783 DBA/2J F B1 1 1 DBA/2J F 251197818090 35768 B6D2F1 M B1 1 609 B6D2F1 M 251197817934 35769 B6D2F1 F B1 1 96 B6D2F1 Unknown 251197817935 35770 BXD1 M 1 9 BXD1 M 251197817936 35771 BXD12 F 1 13 BXD12 F 251197817937 35772 BXD23 M 1 24 BXD23 M 251197817938 35773 BXD34 F 1 43 BXD34 F 251197817939 35774 BXD28 M 1 29 BXD28 M 251197817940 35775 BXD29 F 1 30 BXD29 F 251197817941 35776 BXD39 M 1 54 BXD39 M 251197817942 35777 BXD40 F 1 59 BXD40 F 251197817943 35778 BXDA10 M 1 500 BXD77 M 251197817959 35779 BXD8 F 1 613 BXD8 F 251197817960 35509 C57BL/6J M B2 2 8 C57BL/6J M 251197818158 35529 C57BL/6J M B2R 2 8 C57BL/6J M 251197818086 35578 C57BL/6J F B2 2 5 C57BL/6J F 251197818159 35535 DBA/2J F B2 2 1 DBA/2J F 251197818160 35536 DBA/2J M B2 2 4 DBA/2J M 251197818161 35537 DBA/2J F B2(3) 2 3 DBA/2J F 251197818162 35538 C57BL/6J F B2(7) 2 7 C57BL/6J 2F, 1M 251197818163 35528 B6D2F1 M 2 603 B6D2F1 M 251197818084 35539 B6D2F1 F 2 601 B6D2F1 F 251197818177 35540 BXD11 M 2 12 BXD11 M 251197818178 35541 BXD13 F 2 16 BXD13 F 251197818179 35542 BXD21 M 2 21 BXD21 M 251197818180 35543 BXD24 F 2 25 BXD24 F 251197818181 35514 BXD31 M 2 34 BXD31 M 251197817944 35515 BXD32 F 2 36 BXD32 F 251197817945 35516 BXD42 M 2 63 BXD42 M 251197817946 35517 BXD5 F 2 65 BXD5 F 251197817947 35527 BXDAP15 M 2 79 BXD62 M 251197817948 35531 BXDAP19 F 2 81 BXD43 F 251197818085 35916 C57BL/6J M B3 3 506 C57BL/6J M 251197817964 35932 C57BL/6J M B3R 3 506 C57BL/6J M 16011978011862 35917 DBA/2J M B3 3 509 DBA/2J M 251197817966 35918 C57BL/6J F B3 3 5 C57BL/6J F 251197817967 35919 DBA/2J F B3 3 1 DBA/2J F 251197817968 35920 C57BL/6J F B3(605) 3 605 C57BL/6J F 251197817969 35921 B6D2F1 F B3 3 602 B6D2F1 F 251197817970 35922 B6D2F1 M B3 3 702 B6D2F1 M 251197817971 35923 BXD14 M 3 17 BXD14 M 251197817972 35924 BXD15 F 3 19 BXD15 F 251197817973 35933 BXD33 M 3 39 BXD33 F or M 251197818091 35925 BXD9 F 3 70 BXD9 F 16011978011756 35926 BXD38 F 3 52 BXD38 F 16011978011757 35927 BXD36 M 3 46 BXD36 M 16011978011758 35928 BXD6 M 3 69 BXD6 M 16011978011759 35929 BXDA23F14 F 3 73 BXD86 F or M 16011978011760 35930 BXDAP5F21 M 3 86 BXD60 M 16011978011860 35931 BXDAP6F16 F 3 87 BXD44 F 16011978011861 35549 C57BL/6J F B5 5 5 C57BL/6J F 251197817949 35587 C57BL/6J F B5R 5 5 C57BL/6J F 251197818022 35550 DBA/2J F B5 5 1 DBA/2J F 251197817950 35558 BXD1 F 5 11 BXD1 F 251197818036 35551 BXD12 M 5 14 BXD12 M 251197817952 35552 BXD13 M 5 15 BXD13 M 251197817953 35584 BXD15 M 5 18 BXD15 M 251197818034 35557 BXD28 F 5 28 BXD28 F 251197818035 35585 BXDA10 F 5 499 BXD77 F 251197818037 35586 BXDAP11 M 5 76 BXD51 M or F 251197818038 35553 BXDAP5 F 5 84 BXD60 F 251197818019 35554 BXDA22 M 5 513 BXD85 F 251197818020 35555 BXDAP12 F 5 515 BXD45 F 251197818021 35786 C57BL/6J F B6 6 5 C57BL/6J F 251197818004 35800 C57BL/6J F B6R 6 5 C57BL/6J F 251197818005 35787 DBA/2J F B6 6 1 DBA/2J F 251197818006 35788 C57BL/6J M B6(507) 6 507 C57BL/6J M 251197818007 35789 DBA/2J M B6(510) 6 510 DBA/2J M 251197818008 35790 BXD34 M 6 42 BXD34 M 251197818114 35795 BXD21 F 6 20 BXD21 F 251197818115 35791 BXD24 M 6 26 BXD24 M 251197818116 35792 BXD33 F 6 40 BXD33 F 251197818117 35793 BXD9 M 6 71 BXD9 M 251197818118 35794 BXD31 F 6 32 BXD31 F 251197818119 35796 BXD2 F 6 612 BXD2 F 251197818120 35797 BXDAP6F16 M 6 502 BXD44 M 251197818121 35798 BXDAP8F21 M 6 512 BXD48 M 251197818122 35799 BXDA22F14 M 6 514 BXD85 M or F 251197818123 35566 C57BL/6J F B7 7 5 C57BL/6J F 251197818023 35577 C57BL/6J F B7R 7 5 C57BL/6J F 251197818156 35567 DBA/2J F B7 7 1 DBA/2J F 251197818069 35575 DBA/2J M B7 7 511 DBA/2J M 251197818070 35568 BXD29 M 7 31 BXD29 M 251197818071 35569 BXD36 F 7 47 BXD36 F or M 251197818072 35570 BXD38 M 7 51 BXD38 M 251197818073 35571 BXD39 F 7 56 BXD39 F 251197818124 35572 BXD40 M 7 60 BXD40 M 251197818125 35573 BXD42 F 7 62 BXD42 F 251197818126 35574 BXD5 M 7 66 BXD5 M 251197818127 35579 BXD6 F 7 68 BXD6 F 251197818128 35576 BXDAP15 F 7 78 BXD62 F or M 251197818155 35508 BXDAP19 M 7 82 BXD43 M 251197818157

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 NCBIM32 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 in generating probes position data.

    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.

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.