Bioinformatics approaches to single-blastomere transcriptomics

The totipotent zygote gives rise to cells with differing identities during mouse preimplantation development. Many studies have focused on analyzing the spatio-temporal dependencies during these lineage decision processes and much has been learnt by tracing transgenic marker gene expression up to the blastocyst stage and by analyzing the effects of genetic manipulations (knockout/ overexpression) on embryo development. However, until recently, it has not been possible to get broader overviews on the gene expression networks that distinguish one cell from the other within the same embryo. With the advent of whole genome amplification methodology and microfluidics-based quantitative RT-PCR it became possible to generate transcriptomes of single cells. Here we review the current state of the art of single-cell transcriptomics applied to mouse preimplantation embryo blastomeres and summarize findings made by pioneering studies in recent years. Furthermore we use the PluriNetWork and ExprEssence to investigate cell transitions based on published data.