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Transcriptomic data of parent and NAPE-PLD deteled Caco-2 cells

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE116213 | GEO | 2021/06/23

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study is to evaluate the impact of LXRa phosphorylation at S196 in immune cells on atherosclerosi and obesity, on gene expression via RNA-seq. Lab Methods: Bone marrow from LXRa WT and S196A mice was transplanted into Ldlr-/- mice, which were fed a high fat, high cholesterol diet for 16 weeks prior to evaluation of atherosclerosis and obesity. Plaque CD68+ and T cells, and pWAT macrophages and T cells mRNA profiles of LXRa WT and S196A mice were generated by RNA-seq using Illumina HiSeq 2500 (plaque CD68+ samples) or HiSeq 4000 (Plaque T cells and pWAT FBC, FB and T cells samples). Bioinformatics Methods: Quality control and Illumina adapter removal was performed on the raw sequencing output, followed by mapping of each read pair to the GRCm38.96 transcriptome in order to generate the mRNA profile of each sample. Sample groups from different tissues as well as groups from wild-type or mutant samples were compared against each other for differential gene expression. Results: we analyzed genes differentially expressed in plaque LXRa S196A and found that LXRa S196A induced 365 and repressed 205 genes in CD68+ (LogFC > 0.6, p-value < 0.05), and induced 1,578 genes and repressed 2,392 genes in plaque T cells compared to LXRa WT (LogFC > 1, FDR < 0.05). In pWAT, LXRa S196A vs WT analysis showed that LXRa S196A repressed 419 genes and induced 379 genes in FBC, induced 182 genes and repressed 228 genes in FB, and 624 genes were induced and 622 genes were repressed in LXRa WT (LogFC > 1, FDR < 0.05). Conclusions: This study is the first detailed analysis of plaque and pWAT immune cells transcriptomes from LXRa S196A in bone marrow cells of LDLR-/- mice under high fat and high cholesterol diet, generated by RNA-seq. We demonstrated that LXRa S196A is largely affecting transcriptome of immune cells in atherosclerotic plaque and pWAT. The transcriptome remodeling observed is tissue and cell specific, and controls atherosclerosis and obesity progression.

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Transcriptomic data of parent and NAPE-PLD deteled Caco-2 cells

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