RNA-seq analysis of BORIS/CTCFL knockdown in K562 cell line

The study involved transcriptome analysis using RNA-seq knockdown of BORIS/CTCFL gene expression in K652 cancer cell line using inducible shRNA. The K562 cell line is the only cancer cell line that is known to be dependent on BORIS for proliferation and self-renewal of stemness. The goal of the study was to investigate the early/immediate transcriptional response to BORIS downregulation (over 10-fold reduction in protein level) using an inducible shRNA. Overall design: The K562 cells were stably infected with pLKO-Tet-On-neo vector (empty vector, EV, 3 control replicates) or with the same vector expressing anti-BORIS shRNA (knockdown, KD, 4 independent replicates).