RNA-seq analysis of single bovine blastocysts

BMC Genomics

Research Article

James L Chitwood¹  Pablo J Ross¹  Gonzalo Rincon¹  Juan F Medrano¹  German G Kaiser² 

[1] Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA, USA;Laboratorio de Biotechnología de la Reproducción, INTA, Balcarce, Argentina;

关键词: RNA-seq;    Bovine;    Embryo;    Blastocyst;    SNP;    ASE;   

DOI  :  10.1186/1471-2164-14-350

 received in 2012-11-06, accepted in 2013-05-14,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundUse of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect.ResultsWe report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts.ConclusionsThis study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression.

【 授权许可】

Unknown   
© Chitwood et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.