Analysis of gene expression profiles in INO80-, hIes2-, hIes6-, and hArp8- siRNA knockdown HeLa cells.

To verify the siRNA knockdown efficiency, cells were transfected with 20pmol indicated siRNAs and non-targeting siRNA (siNT, as control). 48 hours after transfection, cells were harvested and lysed for immunoblotting, RT-qPCR, and DNA microarray analysis (DNA microarray was performed once). Total RNA was isolated with Trizol (Invitrogen), and the specific gene expression (all signals normalized to siNT) was measured by RT-qPCR (A). Whole-cell extract (WCE) was prepared by adding 4 × SDS loading buffer. Specific proteins were detected by western blot (WB) with indicated antibodies (B). Overlapping of differentially expressed genes (DEGs) in INO80-, hIes2-, hIes6- and hArp8-siRNA knockdown HeLa cells. DEGs between the knockdown samples and siNT control were assessed by the Illumina Custom differential expression algorithm that was conducted by software package Genomestudio V2011. Then, entrez gene IDs were exploited for Venn diagram plotting including 2159 genes for Ies2, 1936 genes for INO80, 2707 genes for Ies6, and 1445 genes for Arp8 (C).