Transcriptional profiling to compare gene expression in supraorbital mesenchyme (SOM) and early migration mesenchyme (EMM) of wild type mouse embryos

During embryonic development, the mesenchyme surrounding the brain (cranial mesenchyme) gives rise to several structures such as the meninges, calvaria, and the dermis of the scalp. It has been known that the two regions within the cranial mesenchyme, namely, SOM on the basolateral side and EMM on the apical side of the head, have different developmental fates. However, the molecular genetic basis underlying this difference had been unclear. To address this question, we sought to identify genes differentially expressed between EMM and SOM. Through RNAseq, we identified 1095 genes with higher expression in EMM than in SOM, and 398 genes with higher expression in SOM than in EMM (fold change>2, p<0.001, base mean count>50). EMM and SOM were dissected from E12.5 wild type C57BL/6 embryos. 4 EMM samples and 4 SOM samples were used for RNAseq, where each sample was a pool of tissue from 4 to 5 embryos.