Next Generation Sequencing Analyzes Transcriptome after TMEM126A overexpression and knockdown

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify the differential expression genes after TMEM126A overexpression or knockdown. Methods:Total cell mRNA profiles of TMEM126A-knockdown MDA-MB-231 cells (sh-NC vs shT126A) and TMEM126A-overexpression MCF10-Ca1a cells(pCDH vs T126A) were generated by deep sequencing, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment and qRT–PCR validation was performed using SYBR Green assays. Conclusions: Our study represents the first detailed analysis of TMEM126A overexpression and knockdown transcriptomes, with 2 cell lines, generated by RNA-seq technology. Our results show that NGS offers a comprehensive information for the downstream molecular mechanism. Overall design: Using Next Generation Sequencing to analyze the differential gene expression beteewn pCDH vs TMEM126A overexpression in MCF10-Ca1a and sh-NC vs TMEM126A knockdown in MDA-MB-231.