UNC Agilent G4121A Liver Database (Jan06 Freeze) Orig LOWESS

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.