Distinctive Interactomes of RNA polymerase II phosphorylation during different stages of transcription

To investigate the whole-transcriptome effects of Calcium Homeostasis Endoplasmic Reticulum Protein (CHERP)/SCAF6 which specifically binds to the Ser2 of C-terminal domain of RNA Polymerase II, we established HEK293 cell line in which SCAF6 gene was knocked down by shRNA. We then performed gene expression and alternative splicing profiling using data obtained from RNA-seq of 2 cell lines (HEK293 Control vs HEK293 SCAF6 KD). Comparative gene expression and alternative splicing analysis of RNA-seq data for HEK293 cells and its SCAF6 knockdown (HEK293 shSCAF6), two biological replicates per cell line.