Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA-sequencing

Here, we apply differential transcriptome analysis on microscopically isolated cell populations, to define five transcriptional programs that represent each transient embryonic zone and the progression between these zones. The five transcriptional programs contain largely uncharacterized genes in addition to transcripts necessary for stem cell maintenance, neurogenesis, migration, and differentiation. Additionally, we found intergenic transcriptionally active regions that possibly encode novel zone-specific transcripts. Finally, we present a high-resolution transcriptome map of transient zones in the embryonic mouse forebrain. Overall design: mRNAseq performed after laser microdissection of cells from transient embryonic zones in the mouse cortex