title: Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.
abstract: 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.
authors.affiliation: Agrocampus Ouest, Unité Mixte de Recherche 1348 Pegase, F-35000 Rennes, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lagarrigue
authors.forename: Lisa
authors.initials: L
authors.lastname: Martin
authors.forename: Farhad
authors.initials: F
authors.lastname: Hormozdiari
authors.forename: Pierre-François
authors.initials: PF
authors.lastname: Roux
authors.forename: Calvin
authors.initials: C
authors.lastname: Pan
authors.forename: Atila
authors.initials: A
authors.lastname: van Nas
authors.forename: Olivier
authors.initials: O
authors.lastname: Demeure
authors.forename: Rita
authors.initials: R
authors.lastname: Cantor
authors.forename: Anatole
authors.initials: A
authors.lastname: Ghazalpour
authors.forename: Eleazar
authors.initials: E
authors.lastname: Eskin
authors.forename: Aldons J
authors.initials: AJ
authors.lastname: Lusis
mesh_terms: D000483:Alleles; D000818:Animals; D000971:Antineoplastic Combined Chemotherapy Protocols; D003433:Crosses, Genetic; D003520:Cyclophosphamide; D005047:Etoposide; D005260:Female; D015870:Gene Expression; D008040:Genetic Linkage; D018392:Genomic Imprinting; D008099:Liver / Q000378:metabolism*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008942:Mitoxantrone; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D011241:Prednisone; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA
chemical_list: D005047:Etoposide; D003520:Cyclophosphamide; D008942:Mitoxantrone; D011241:Prednisone
keywords: RNA-Seq; allele-specific expression; genomic imprinting; linkage analysis
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