Open AccessAnalysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage
Author(s) -
Sandrine Lagarrigue,
Lisa Martin,
Farhad Hormozdiari,
PierreFrançois Roux,
Calvin Pan,
Atila van Nas,
Olivier Demeure,
Rita M. Cantor,
Anatole Ghazalpour,
Eleazar Eskin,
Aldons J. Lusis
Publication year - 2013
Publication title -
genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.792
H-Index - 246
eISSN - 1943-2631
pISSN - 0016-6731
DOI - 10.1534/genetics.113.153882
Subject(s) - expression quantitative trait loci , biology , genetics , allele , gene , quantitative trait locus , rna seq , rna , genomic imprinting , gene expression , genetic linkage , transcriptome , genotype , single nucleotide polymorphism , dna methylation
We report an analysis of allele-specific expression (ASE) and parent-of-origin expression in adult mouse liver using next generation sequencing (RNA-Seq) of reciprocal crosses of heterozygous F1 mice from the parental strains C57BL/6J and DBA/2J. We found a 60% overlap between genes exhibiting ASE and putative cis-acting expression quantitative trait loci (cis-eQTL) identified in an intercross between the same strains. We discuss the various biological and technical factors that contribute to the differences. We also identify genes exhibiting parental imprinting and complex expression patterns. Our study demonstrates the importance of biological replicates to limit the number of false positives with RNA-Seq data.
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