mRNA sequencing of the global effect of SOX2 on gene expression in hESC and hESC derived NPCs.. Homo sapiens

Global transcriptome analysis reveals that SOX2 regulates a common group safeguarding stem cell identity in hESCs and hNPCs, and also distinct functional groups regulating diverse cell type dependent developmental processes in hESCs and hNPCs, sheding light on the mechanism underlying SOX2's dynamic function in the two related stem cell types. Overall design: To analyze the global effect of SOX2 on gene expression in hESC and hNPC, we analyzed the gene expression profiles upon SOX2 KD in hESC and hNPC. Due to the compensation effect of SOX3 in hESC, we used non-targeting siRNA (siNT) and two sets of siRNAs targeting both SOX2 and SOX3 (siSOX2/3-1 and siSOX2/3-2) to knock down both SOX2 and SOX3 in hESC and compared the gene expression profile between siNT and siSOX2/3 by RNA-seq. We also compared the gene expression profiles in hNPC treated with siNT and two SOX2 siRNAs (siSOX2-1 and siSOX2-2) by RNA-seq.