Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [scRNA-Seq]
Purpose:One goal of this single RNA-seq is to compare scRNA  profiles in gastric organoids cultured in CM and differentiation media including  EB,  BI 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 were sorted by flow cytometry.ScRNA-seq libraries were generated using the Chromium Single Cell 3' Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: By comparing scRNA-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. Overall design: Single cell RNA profiles of organoids in CM and differentiation medium detected after 2 days culture.