Expression profile of PIK3R1 knockout and non-targeting control cells in response to Notch inhibition

To gain insights how loss of PIK3R1 confers resistance to pharmacological Notch inhibition in T-ALL cells, we performed gene expression analysis. Libraries for mRNA-seq were prepared with the Stranded mRNA Ligation method (Illumina) starting from 1µg RNA, according to manufacturer's instructions. Libraries, all bearing unique dual indices, were subsequently loaded at 250pM in a HiSeq 4000 instrument (Illumina) and sequenced according to manufacturer's instructions, yielding paired-end reads of 75 nucleotides. Reads were trimmed of their adapters with bcl2fastq v2.20 (Illumina) and quality-controlled with FastQC v0.11.9. PIK3R1 deficiency leads to up-regulation of cell cycle and pro-survival genes in response to Notch inhibition. Overall design: Expression profile comparing PIK3R1 knockout and non-targeting control RPMI-8402 cells in response to Notch inhibitor CB-103 or GSI (LY3039278) for 24hrs. Experiments are set up in triplicates.