Next Generarion sequencing identifing changes of gene expression mediated by ectopic GFI1 expression or CRISPR-mediated IKAROS knockout

To identify changes in gene expression associated with either ectopic GFI1 expression or CRISPR-mediated IKAROS knockout, we applied bulk RNA-Seq with GFI1-3XFLAG CCRF-CEM cells. Wild type or IKAROS knockout cells were treated with vehicle or doxycycline for 24 hours. Between 21.7 and 28.2 million RNA-Seq reads were generated for each condition, 88.6 to 90.3% of which aligned uniquely to the human Hg38 reference genome. ~99% of the reads within coding regions aligned to the correct strand. Hierarchically clustering the top 500 most significantly differentially regulated genes across all the conditions (ranked based on p-value) revealed groups of genes repressed and activated by the different manipulations. mRNA profiles of WT or IKAROS KO CCRF-CEM cells inducibly expressing GFI1(Doxycycline) or not (PBS)