Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [RNA-Seq]

Purpose:One goal of this bulk RNA-seq is to compare genome-wide transcriptome profiles in gastric organoids cultured in CM and differentiation media including Nog WD, BMP4, EB, Isx-9, BI, NRC and NRCA in mouse and EB, NRCSI and BIMDP in human. The other aim is to identify the differential biological process underpinning gastric epithelial cell differentiation and the conservative or divergent process between human and mouse. Methods: For human and mouse gastric organids, we isolated and digested with Tryple and then extracted total RNA. Bulk RNA-seq was performed using the Illumina Hiseq X. Sequence reads that passed quality filters were analysed at the transcript isoform level using two methods: Burrows-Wheeler Aligner (BWA) followed by ANOVA and TopHat followed by Cufflinks. Results: By comparing RNA-seq data, we identified the signature genes involved in gastric epithelial cell lineage and enrichment of biological processes during differentiation. Conclusion: EB is optimal medium for pit cell differentiation in both human and mouse, BI and BIMDP media are optimal media for parietal cell differentiation in human and mouse respectively, NRCS and NRCSI media are optimal media for chief cell differentiation in human and mouse respectively.