Transcriptomics

Dataset Information

307

RNA-seq of liver samples from C57BL/6J, CAST/EiJ mice as well as their initial and reciprocal F1 progeny to study the compensatory cis-trans regulation of liver gene expression


ABSTRACT: Two inbred mouse strains, C57BL/6J and CAST/EiJ, were crossed to generate both initial and reciprocal F1 crosses. For each genetically distinct class of mice (F0 C57BL/6J, F0 CAST/EiJ, F1i - C57BL/6J x CAST/EiJ, F1r - CAST/EiJ x C57BL/6J, where the male parent is listed first), samples were collected from a single lobe of the liver from 6 male mice between the ages of 4 and 6 months. The 24 samples were then processed to generate strand-specific RNA-seq libraries, which were sequenced on the Illumina GAII platform using 72bp paired-end reads.

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Mus musculus  

SUBMITTER: Angela TF Goncalves  

PROVIDER: E-MTAB-1091 | ArrayExpress | 2012-09-07

SECONDARY ACCESSION(S): ERP001401

REPOSITORIES: ArrayExpress, ENA

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Publications

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

Goncalves Angela A   Leigh-Brown Sarah S   Thybert David D   Stefflova Klara K   Turro Ernest E   Flicek Paul P   Brazma Alvis A   Odom Duncan T DT   Marioni John C JC  

Genome research 20120823 12


Gene expression levels are thought to diverge primarily via regulatory mutations in trans within species, and in cis between species. To test this hypothesis in mammals we used RNA-sequencing to measure gene expression divergence between C57BL/6J and CAST/EiJ mouse strains and allele-specific expression in their F1 progeny. We identified 535 genes with parent-of-origin specific expression patterns, although few of these showed full allelic silencing. This suggests that the number of imprinted ge  ...[more]

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