![]() High-throughput sequencing of RNA (RNA-seq) quantifies transcripts expressed from known genes with an enormous dynamic range and discovers transcriptional units that are biologically novel yet previously unannotated, or not fully characterized in available databases or gene expression arrays. Transcriptome sequencing describes global trends in gene expression while also detailing alterations to biological pathways at the gene-specific level. This 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. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. ![]() Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. 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). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. We 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). 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. Use 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.
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