Complete Transcriptome Analysis by 5′-End Single-Cell RNA-Seq with Random Priming

Single-cell transcriptome analysis reveals heterogeneous cell types in complex tissues and leads to unexpected biological findings when compared to bulk populations. However most of the methods focus on the 3′-end of polyadenylated transcripts using droplet-based technology. To achieve complete transcriptome, we describe single-cell 5′-end transcriptome protocol with random primed-cDNA harvesting on the Fluidigm C1™ platform which can isolate and process up to 96 cells from a single run with custom library preparation. The method enables detection of Transcription Start Site (TSS) at the single-cell resolution yielding a more comprehensive overview of gene regulatory elements governing in the EpiSC-like cell (EpiLC) including non-polyadenylated RNA and enhancer RNA activities.