Whole transcriptome sequencing of E18 mouse cortex

We observed Csmd3-deficient mice exhibited growth retardation, atypical learning and memory behaviors. Futher, cortical neurons from mice lacking Csmd3 showed abnormal development. To identified the role of Csmd3 in cortex develepement, we performed whole transcriptome sequencing on embryonic 18 days cortex from Csmd3-/- and wild type mice. As a result, a total of 2133 differentially expressed genes (DEGs) were identified, including 1400 upregulated genes and 733 downregulated genes. Downregulated DEGs were mainly related to synaptic functions, while the upregulated DEGs were involved in multiple progresses related to cell-to-cell communication. In terms of cell type preference as referring to the single cell sequencing data in mouse neocortex at E18, downregulated DEGs were exlusively enriched into neurons and upregulated DEGs were involved with multiple cell types. Our study is the first detailed analyses of Csmd3 in development mouse cortex, identifing Csmd3 plays a pivotal role in synaptic organazation and transmission, also has an effect on glia-vascular inter-cellular communication. Total mRNA profiles of E18 WT, Csmd3-/- cortex by deep sequencing using Illumina NovaSeq 6000.