Pluto Bioinformatics

GSE157110: High throughput RNA-sequencing identifies Differentially Expressed Genes (DGS) of control and shATXN7L3 HCCLM3 cells

Bulk RNA sequencing

Purpose: High throughput RNA-seq has provided an efficient and convenient access to screening substantial differentially expressed genes (DEGs). The goals of this study are to screen out ATXN7L3-regulated DEGs of HCC cells by utilizing RNA-sequencing and to furtherly identify specific biological function-related gene subset from ATXN7L3-regulated DEGs; Method: Firstly, HCCLM3 cells were seperated into two groups and respectively transfected with lentivirus-delivered shATXN7L3 and shcontrol. We cultured these cells with DMEM containing 10% FBS serum. 48 hours later, cells of two groups were harvested by Trizol RNA isolater and analyzed by High througput RNA-sequencing.; Conclusion: Using next generation high throughput RNA-sequencing technology, we identified a total of 3831 genes were significantly changed after ATXN7L3 knockdown. There were 1914 ATXN7L3 positive-regulated genes and 1917 ATXN7L3 negative-regulated genes. Then we focused on top DEGs using 0.8-log2(fold change) as a cutoff for statistic analysis. Furtherly, 246 positive-regulated DEGs and 187 negative-regulated DEGs were identified. Finally, pathway and process enrichment analysis identified a series of cell growth-related DEGs. SOURCE: Ning Sun (wangchunyu-cmu@hotmail.com) - Chromatin biology laboratory China Medical University

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