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This study aimed to develop a method to evaluate the quality of bovine in vitro fertilized (IVF) embryos based on gene expression profiling via whole-transcriptome amplification. The expression of 11 developmentally important genes in individual bovine in vivo-derived (IVD) and IVF embryos were examined. Gene expression profiling was conducted by classifying the expression level of each gene in individual embryos as low, medium, or high. The IVF group had a higher (P < 0.01) proportion of embryos with low expression of SOX2, NANOG, and FGF4. In addition, a correlation analysis between the expression levels of each gene in individual embryos demonstrated that the relationship between gene expression differed with respect to IVD and IVF embryos. Our results suggest that the expression profiling of developmentally important genes using IVD embryos as normal controls could be a useful indicator for evaluating the quality of bovine IVF embryos. [ABSTRACT FROM AUTHOR]

Single-cell analysis gives insights into the heterogeneity of neighboring cells within tissues or within cell populations and is increasing in importance in life science and medicine. Genome and transcriptome sequencing require orders of magnitude of more starting material than what is found in an individual cell. Handling such small quantities means that degradation, sample loss, and contamination can have a pronounced effect on sequence quality and robustness. Recent technical advances in amplification have helped mitigate these challenges. Single-cell sequencing addresses studies of rare cell types, heterogeneous samples, phenotypes associated with mosaicism or variability, and microbes that cannot be cultured. Single-cell sequencing can enable the discovery of clonal mutations, cryptic cell types, or transcriptional features that would be diluted or averaged out in bulk tissue. This unit describes the entire workflow from cells to next-generation sequencing (NGS), including cell lysis, MDA-based whole-genome and whole-transcriptome amplification, and NGS library preparation. © 2016 by John Wiley & Sons, Inc., (Copyright © 2016 John Wiley & Sons, Inc.)