Deep transcriptional profiling of longitudinal changes during neurogenesis and network maturation in vivo. Mus musculus domesticus

Using next generation, paired-end RNA sequencing, we have quantified the deep transcriptional changes that occur during differentiation of murine embryonic stem cells i(ESCs) nto a highly enriched population of glutamatergic cortical neurons. RNA was isolated and sequenced from ESCs (DIV -8; n=4); neuroepithelial stem cells (DIV -4; n=3); radial glia (DIV 0; n=3); developmental stage (DS) I/II neurons (DIV 1; n=4); DS III/IV neurons (DIV 7; n=5); and maturing DS IV/V neurons at DIV 16 (n=4); DIV 21 (n=4); and DIV 28 (n=4). These data provide a detailed and nuanced account of longitudinal changes in the transcriptome over eight stages of neurogenesis and neuronal maturation, starting from mouse embryonic stem cells and progressing through neuroepithelial stem cell induction, radial glial cell formation, neurogenesis, neuronal maturation and cortical patterning. Understanding the transcriptional mechanisms underlying the differentiation of stem cells into mature, glutamatergic neurons of cortical identity has myriad applications, including the elucidation of mechanisms of cortical patterning; identification of neurogenic processes; modeling of disease states; detailing the host cell response to neurotoxic stimuli and determination of potential therapeutic targets. In future work we anticipate correlating changes in longitudinal gene expression to other cell parameters, including neuronal function as well as characterizations of the proteome and metabolome. In this data article we describe the methods used to produce this data and present the raw sequence read data in FASTQ files, sequencing run statistics and a summary flatfile of raw counts for 22,164 genes across 31 samples, representing 3-5 biological replicates at all time points. We believe this data is a valuable contribution to diverse research efforts in bioinformatics, stem cell research and developmental neuroscience studies.