GSE116213
Transcriptomic data of parent and NAPE-PLD deteled Caco-2 cells
PURPOSE: We generated NAPE-PLD-deleted Caco-2 cells, which is a model of intestinal epithelial cells, using genome editing with the CRISPR/Cas9 system. To explore the molecular events following the deletion of NAPE-PLD in Caco-2 cells, we examined the transcriptomic changes in the NAPE-PLD deleted clone 35 compared with Caco-2 parent cells by RNA-seq. METHODS: mRNA profiles of parent and NAPE-PLD deleted Caco-2 cells were generated using Illumina HiSeq4000 (n=2/each cell). Those raw sequence data were then mapped to the human hg38 reference genome using a custom MOIRAI pipeline with STAR 2.51 for alignment. Then, read counts for each transcript were obtained using featureCounts, and the raw count data were directly analyzed for differential gene expression by using edgeR 3.20.9. RESULTS: Approximately 40 million reads per sample were obtained as raw data. Among a total of 12,331 genes detected in at least in one cell type, 1,019 genes were up-regulated (FDR < 0.01, logFC > 1) and 827 genes were down-regulated (FDR < 0.01, logFC > 1) in clone 35 compared with the parental cells. Overall design: mRNA profiles of parent and NAPE-PLD deleted Caco-2 cells were generated using Illumina HiSeq4000.