RNA-seq mouse intestines from PN, Germ-free, SPF and Antibiotics-treated mice

We hypothesized that there were genes involved in the maintenance of intestinal tolerance to commensal bacteria. These genes should meet the following criteria: expressed in intestines, upregulated in the presence of commensal bacteria and downregulated in absence of microbes. To find these genes, we collected small intestines from postnatal mice that neither affected by the bacteria nor by the food, adult mice bred in germ-free or specific pathogen-free conditions, and adult SPF mice treated with antibiotics. We therefore performed bulk RNA sequencing using these cells.本研究提出假说：存在参与维持机体对共生细菌的肠道免疫耐受的基因。此类基因需满足以下筛选标准：在肠道组织中表达、于共生细菌存在时呈上调表达、在无微生物环境中呈下调表达。为筛选得到此类基因，本研究采集了三类小鼠小肠样本：未受细菌与食物影响的新生小鼠小肠、饲养于无菌（germ-free）或无特定病原体（specific pathogen-free, SPF）环境中的成年小鼠小肠，以及经抗生素处理的成年SPF小鼠小肠。随后针对上述样本开展批量RNA测序（bulk RNA sequencing）实验。