Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage-Reference-Cited by-同舟云学术

Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage

Published:2013-11-01 Issue:3 Volume:195 Page:1157-1166
ISSN:1943-2631
Container-title:Genetics
language:en
Short-container-title:

Author:

Lagarrigue Sandrine¹²³,Martin Lisa⁴,Hormozdiari Farhad⁵⁶,Roux Pierre-François¹²³,Pan Calvin⁴⁶,van Nas Atila⁶,Demeure Olivier¹²³,Cantor Rita⁶,Ghazalpour Anatole⁶,Eskin Eleazar⁵⁶,Lusis Aldons J⁴⁶⁷

Affiliation:

1. Agrocampus Ouest, Unité Mixte de Recherche 1348 Pegase, F-35000 Rennes, France

2. Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1348 Pegase, F-35000 Rennes, France

3. Université Européenne de Bretagne, Rennes, France

4. Department of Medicine/Division of Cardiology, University of California, Los Angeles, California 90095-1489

5. Department of Computer Sciences, University of California, Los Angeles, California 90095-1489

6. Department of Human Genetics, University of California, Los Angeles, California 90095-1489

7. Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095-1679

Abstract

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.

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

https://academic.oup.com/genetics/article-pdf/195/3/1157/42119506/genetics1157.pdf

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