Various single cell RNA-Seq technologies have been developed recently. However, most of these techniques are based on performing tens of microliters reactions in eppendorf tubes, making them prone to contamination. Here we develop a microfluidics-based technology for single cell RNA-Seq transcriptome analysis. This new method performs the majority of the reaction steps at nanoliter volume within sealed chambers on-chip, eliminating potential contaminations and sophisticated manual handling. We show that our method is highly sensitive and can detect as many as 12,684 genes expressed in an individual mouse embryonic stem cell (mESC). We have also detected 214 long non-coding RNAs (lncRNAs) specifically expressed in ESCs and not in mouse embryonic fibroblasts (MEFs). Moreover, the high accuracy of this method allows us to clearly identify the crucial expression details such as alternative polyadenylation (APA) and alternative splicing (AS) events within individual cells, and to discover the expression heterogeneity at the single cell level. This technology will facilitate the dissection of transcriptome complexity and heterogeneity of pluripotent stem cells or any other types of mammalian cells. SOURCE: Xiannian Zhang (friedpine@gmail.com) -  Peking University

Pluto Bioinformatics

GSE47835: Microfluidics facilitated RNA-Seq transcriptome analysis of single mouse embryonic stem cells