UNC Agilent G4121A Liver Database (Jul04 Freeze) Orig LOWESS

Accession number: GN34

    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.