Single cell transcriptomics: Fluidigm scRNA-seq and C1 CAGE revealed distinct phases of pluripotency during na?ve-to-primed conversion in mice

In this study transcriptome dynamics of the na?ve to primed stem cell transition process have been investigated at the single-cell level in a mouse model system using C1 single-cell RNA-seq and C1-CAGE (single-cell Cap analysis of gene expression) on the Fluidigm platform. C1 scRNA-seq allowed the quantification of gene expression in thousands of polyadenylated genes. For complementation, C1-CAGE can detect non-polyadenylated RNAs like non-coding RNAs (e.g. antisense or enhancer-associated RNA). Cell differentiation from na?ve mouse embryonic stem cells (mES) to primed Epiblast stem cells (EpiSC) has been established using a Wnt inhibitor. Samples have been obtained in a time-course starting from undifferentiated mES cells in 24h intervals until day 4. Furthermore, EpiSCs have been sampled to represent the fully primed state.