PolyA RNA-seq from HCT116 (WT and CDK8as/as) cells in normoxia or hypoxia and treated with DMSO or 3MB-PP1

To determine the impact of CDK8 kinase activity on steady-state mRNA levels, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116 (CDK8wt/wt and CDK8as/as) in the presence of absence of 3MB-PP1 to specifically inhibit analog senstitive (as) CDK8. Overall design: PolyA RNA for two independent biological replicates was purified from HCT116 cells (CDK8wt/wt and CDK8as/as) incubated in normoxic (ambient oxygen) or hypoxic (1% oxygen) conditions for 24 hrs and treated with DMSO or the ATP-analog 3MB-PP1, and was sequenced on the Ion Torrent Proton platform. Reads were aligned (GSNAP) to the human genome (hg19) and gene-level counts (HTseq-count) were used for differential expression analysis (DESeq2).