Global transcriptome profiling of SETD2 and hnRNP L depleted cells and H3K36me3 profile of WT 293T cells
We performed RNA-seq of 293T cells post depletion and SETD2 or hnRNP L to compare their global transcriptome profile. We also looked at the distribution of the histone mark H3K36me3 in wild type 293T to correlate it with the observed transcriptome changes upon SETD2 and hnRNP L depletion. We rescued SETD2 knock out 293T cells with SETD2 FL (Full Length), FL?SRI (FLwoSRI) and FL?SHI (FLwoSHI) and performed H3K36me3 ChIP-Seq. Overall design: Wild type 293T cells were used in these studies. For transcriptome analysis, the WT cells were treated with scramble siRNA pool or siRNA pool targetting SETD2 or hnRNP L. The validated siRNAs were procurred from Dharmacon. Cells were treated for 72 hours with the siRNAs before proceeding for RNA extraction. SETD2 knock out 293T cells were used in these studies. The cells were transfected with SETD2 FL, FL?SRI (FLwoSRI) and FL?SHI (FLwoSHI) expressing constrcust under the control of CMV promoter. 72 hours post-transfection cells were fixed and processed for ChIP.