Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach.Methods: mRNA profiles of Sox2 WT and Sox2 KO gastric glands were generated by RNA-sequencing, in triplicate, using a Illumina HiSeq 2500 instrument, resulting in 36 million single-end 50bp reads per smaple. Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq v.0.6.0 (Anders et al., 2015) based on a current Ensembl annotation file for mm10/GRCm38 (release 75).Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of cancer and intestinal related genes.

研究背景：Sox2的表达可标记胃干细胞与祖细胞，这引发了一系列关键科学问题，包括Sox2所调控的靶基因，以及Sox2自身在胃稳态与胃部疾病发生过程中的作用。本研究旨在明确Sox2在胃部中的功能及其所调控的基因。
实验方法：采用Illumina HiSeq 2500测序仪，对Sox2野生型（Wild Type，WT）与Sox2敲除型（Knock Out，KO）小鼠的胃腺体进行RNA测序（RNA-sequencing），设置3次生物学重复，每个样本产出约3600万条单端50bp读长的测序读段。使用STAR软件（Dobin等人，2013年）将测序读段比对至小鼠参考基因组（mm10/GRCm38）；基于mm10/GRCm38的最新Ensembl注释文件（版本75），通过HTSeq v.0.6.0软件（Anders等人，2015年）计算转录本的读段计数。
实验结果：Sox2并非胃干细胞自我更新与上皮稳态维持所必需，但其可调控癌症相关及肠道相关基因的表达。