Transcriptome analysis of human embryonic stem cells (hESCs) upon siRNA-mediated knockdown of hESC-essential genes. Homo sapiens

The maintenance of pluripotency requires the coordinated expression of a set of essential genes. Thorough identification of these genes is vital for gaining a better understanding of the pluripotent state. To this end, we have recently generated a genome-wide loss-of-function library in haploid human pluripotent stem cells utilizing the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology using nearly 180,000 single guide RNAs (sgRNAs) and targeting 18,166 protein-coding genes. By combining the results of our high-throughput genetic screening with the analysis of publicly available RNAseq data of pluripotent stem cells and several somatic cells, we have determined the essential genes which have an enriched expression in hESCs and termed these genes as hESC-essential genes. Here, we have individually knocked down four of these hESC-essential genes with siRNAs, namely SALL4, DSCC1, SEPHS1 and VRTN, in human embryonic stem cells and analyzed the transcriptomes of the cells upon downregulation of these transcripts in order to unravel part of the pathways affected by hESC-essential genes. Overall design: For each of the gene knockdown conditions, three biological replicates were analyzed. hESCs were transfected with commercial pooled siRNAs targeting either of the four genes targeted along with the control siRNAs. Four control conditions included in the study were treated with two independent control siRNAs with two biological replicates for each.