Transcriptional profiling of pre- and post-natal glutamatergic progenitors and nascent neurons by single cell RNA sequencing

Purpose: We labeled synchronous cohorts of prenatal and postnatal glutamatergic progenitors to study their lineage relationship and transcriptional specificities. Method and results: We performed scRNA-seq of postnatal glutamatergic progenitors isolated from microdissected pallium at E15.5 or dorsal subventricular zone at P2 in the mouse. Our results highlight transcriptional dysregulation at P2 which includes genes involved in metabolism, differentition and migration. tdTom+ cells (glutamatergic progenitors) were isolated from E15 and P2 transgenic mice expressing a tamoxifen inducible Cre-recombinase under Neurog2 genomic regulatory sequences. A total of 230 cells were obtained (121 at E15.5 and 109 at P2). Following tissue dissociation, single cells were isolated by flow cytometry and processed with the C1 Single-Cell Auto Prep System (Fluidigm). RNA-sequencing libraries were muliplexed and sequenced at 75bp single reads using the Illumina HiSEQ500 platform at a depth of 7M reads. Every sample in this series represents a single cell.