| Experiment Id | GSE17522 | Name | BXD Mouse Liver Gene Expression |
| Experiment Type | transcription profiling by array | Study Type | Baseline |
| Source | GEO | Curation Date | 2022-03-14 |
| description | The liver is the primary site for the metabolism of nutrients, drugs, and chemical agents. Although metabolic pathways are complex and tightly regulated, genetic variation among individuals, reflected in variations in gene expression levels, introduces complexity into research on liver disease. This study dissected genetic networks that control liver gene expression through the combination of large-scale quantitative mRNA expression analysis with genetic mapping in a reference population of BXD recombinant inbred mouse strains for which extensive single-nucleotide polymorphism, haplotype, and phenotypic data are publicly available. We profiled gene expression in livers of naive mice of both sexes from C57BL/6J, DBA/2J, B6D2F1, and 41 BXD strains using Agilent oligonucleotide microarrays. These data were used to map quantitative trait loci (QTLs) responsible for variations in the expression of about 19,000 transcripts. We identified polymorphic local and distant QTLs, including several loci that control the expression of large numbers of genes in liver, by comparing the physical transcript position with the location of the controlling QTL. CONCLUSION: The data are available through a public web-based resource (www.genenetwork.org) that allows custom data mining, identification of coregulated transcripts and correlated phenotypes, cross-tissue, and cross-species comparisons, as well as testing of a broad array of hypotheses. Basal gene expression in the livers of 41 BXD strains, the parentals and the F1 cross, consisting of C57BL/6J, DBA/2J, B6D2F1, BXD1, BXD2, BXD5, BXD6, BXD8, BXD9, BXD11, BXD11TY, BXD12, BXD13, BXD14, BXD15, BXD16, BXD19, BXD21, BXD23, BXD24, BXD28, BXD29, BXD31, BXD32, BXD33, BXD34, BXD36, BXD38, BXD39, BXD40, BXD42, BXD43, BXD44, BXD45, BXD48, BXD51, BXD60, BXD62, BXD69, BXD73, BXD77, BXD85, BXD86, BXD92 pooled from 2-3 mice of the same sex and strain. The arrays were run in 8 batches, balanced by sex and strain with intra- and inter-batch replicates. Interbatch normalization was carried out using a nested analysis of variance mixed model, with samples within each batch crossed with sex and strain. |
