Gene expression comparison between human glioma cells: U87-MG wild-type and CHI3L1 knock-out (clone 1 and 2)

U87-MG human glioma cells were subjected to CRISPR/Cas9 genetic engineering to knock-out CHI3L1 gene. We then compared gene expression profiles between maternal cells (wild-type, WT) and two clones obtained throught CRISPR/Cas9 pipeline: clone 1 (KO1) and clone 2 (KO2) Overall design: We extracted RNA from 3 subsequent cell culture passages after 48h of growth (n=3 for each condition: WT, KO1 and KO2). We assessed the quality of extracted RNA for an RIN of >9. We prepared libraries with KAPA Stranded mRNA-Seq Kit (Roche) and then performed pair-end sequencing: 2x 76 cycles, target number of reads: 25 million per sample on Illumina HiSeq 1500.