ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/049/SRR22864249/SRR22864249_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/050/SRR22864250/SRR22864250_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/054/SRR22864254/SRR22864254_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/053/SRR22864253/SRR22864253_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/041/SRR22864241/SRR22864241_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/042/SRR22864242/SRR22864242_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/047/SRR22864247/SRR22864247_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/040/SRR22864240/SRR22864240_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/048/SRR22864248/SRR22864248_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/043/SRR22864243/SRR22864243_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/049/SRR22864249/SRR22864249_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/046/SRR22864246/SRR22864246_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/042/SRR22864242/SRR22864242_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/045/SRR22864245/SRR22864245_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/052/SRR22864252/SRR22864252_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/051/SRR22864251/SRR22864251_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/054/SRR22864254/SRR22864254_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/055/SRR22864255/SRR22864255_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/057/SRR22864257/SRR22864257_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/055/SRR22864255/SRR22864255_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/040/SRR22864240/SRR22864240_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/047/SRR22864247/SRR22864247_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/048/SRR22864248/SRR22864248_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/057/SRR22864257/SRR22864257_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/056/SRR22864256/SRR22864256_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/053/SRR22864253/SRR22864253_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/046/SRR22864246/SRR22864246_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/043/SRR22864243/SRR22864243_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/044/SRR22864244/SRR22864244_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/041/SRR22864241/SRR22864241_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/056/SRR22864256/SRR22864256_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/052/SRR22864252/SRR22864252_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/045/SRR22864245/SRR22864245_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/051/SRR22864251/SRR22864251_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/044/SRR22864244/SRR22864244_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR228/050/SRR22864250/SRR22864250_1.fastq.gzprimary200OKGenomicsTranslational Data Science Facility, Agora Cancer Research Center & Swiss Institute of Bioinformaticshttps://www.ebi.ac.uk/ena/browser/view/PRJNA915209Homo sapiensTo 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.xref:PubMed:37358480ENAfalseExpression profile of PIK3R1 knockout and non-targeting control cells in response to Notch inhibitionExpression profile of PIK3R1 knockout and non-targeting control cells in response to Notch inhibition2025-09-242023-07-01PRJNA915209GSE221577960637358480