Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE226196 | GEO | 2025/05/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Project description: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.

2025-05-29 | GSE226195 | GEO

Human pluripotent stem cell derived hematopoietic cells using expanded potential stem cell media

Project description:We recently developed a novel chemical media formulation, Expanded Potential Stem Cell Medium (EPSCM), that maintains mouse pluripotent stem cells (PSCs) in a unique cellular state that affords extraembryonic differentiation capacity. Here, we have used EPSCM to stably maintain human PSCs and used EPSCM-maintained iPSCs (EC-EPSCM) to study in vitro hematopoietic differentiation by embryoid body (EB) formation. We found that human PSCs maintained in EPSCM can spontaneously form embryoid bodies and efficiently undergo in vitro hematopoiesis using a simple differentiation protocol. EC-EPSCM PSCs generated primitive-wave and definitive-wave hematopoietic cells, which were chracterized by RNA-sequencing analysis.

2022-04-26 | GSE130662 | GEO

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

Project description:The directed differentiation of adult gastric stem cells into specific epithelial cell types is crucial for gastric homeostasis. Although it is well appreciated that the niche plays a critical role in gastric epithelium cell differentiation, the relevant molecular factors and the underlying regulatory mechanisms remain poorly understood. In this study, by combining the knowledge of the niche cells obtained from single-cell RNA sequencing and manipulation of signaling pathways, we achieved efficient differentiation of various gastric epithelial cell types in mouse and human gastric organoids. These in vitro differentiated cells showed a similar gene expression profile to those in gastric tissues. Specifically, we showed that BMP4 signaling stimulates parietal cell differentiation, EGF and BMP4 signaling work together to enhance pit cell differentiation, while TGF-β inhibition facilitates chief cell differentiation. In addition, the small molecule Isoxazole 9, which has been shown to stimulate differentiation of neuronal cells, pancreatic β-cells, and intestinal enteroendocrine cells, promotes parietal and endocrine cell differentiation in gastric organoids. Our data also revealed the different requirements of parietal and chief cell differentiation between mouse and human. Together, our findings provide a mechanistic insight into gastric epithelial cell differentiation and uncover its similarities and differences between mouse and human.

2025-05-29 | GSE271476 | GEO

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

2025-05-29 | GSE269974 | GEO

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

2025-05-29 | GSE269973 | GEO

EB differentiation study

Project description:EB differentiation study

| PRJNA644196 | ENA

Expression data from Helicobacter pylori isolates infecting a gastric epithelial progenitor cell line

2008-02-22 | GSE10261 | GEO

Metabolomics Workbench ST000354 - GNPS - Metabolite comparison of mouse gastric tissue and glands

Project description:The goal of this project was to compare the metabolite profiles of the: mouse gastric antrum and the mouse gastric corpus, the mouse gastric antrum and the mouse gastric antrum isolated glands, and the mouse gastric corpus and the mouse gastric corpus isolated glands.

2018-08-02 | MSV000082700 | GNPS

Expression data from Helicobacter pylori isolates infecting a gastric epithelial progenitor cell line

Project description:Helicobacter pylori clinical isolates can establish themselves in gastric epithelial stem cells and this interaction may have implications for gastric tumorigenesis. Mouse gastric epithelial progenitor cells (mGEPs) were infected for 24hrs with Helicobacter pylori clinical isolates Kx1 and Kx2. Kx1 and Kx2 were also grown in cell media in the absence of cells. Kx1 was isolated from a patient with chronic atrophic gastritis (ChAG) and Kx2 from the same patient 4 years later, when he progressed to gastric adenocarcinoma. Keywords: RNA Expression Array H. pylori strains Kx1 or Kx2 that had been grown to log phase were used to infect mGEP cells.. After 24h, media and non-attached bacteria were washed off and the cells harvested by trypsinization. RNA was prepared from bacteria infecting mGEP cells or bacterial cultures of Kx1 and Kx2 grown in cell media for 24h in the absence of mGEP cells.

2010-05-26 | E-GEOD-10261 | biostudies-arrayexpress

BI 456906: a dual glucagon-like peptide-1/glucagon agonist promoting bodyweight reduction

Project description:Glucagon and glucagon-like peptide-1 (GLP-1) are hormones involved in energy homeostasis. GLP-1 receptor (GLP-1R) agonism reduces food intake and delays gastric emptying, and glucagon receptor (GCGR) agonism increases energy expenditure by thermogenesis. BI 456906 is a subcutaneous, once-weekly injectable dual GLP-1R/GCGR agonist in development for the treatment of obesity or non-alcoholic steatohepatitis. Here we show that BI 456906 is a potent dual agonist with an extended half-life in human plasma. Key GLP-1R-mediated mechanisms of reduced food intake, delayed gastric emptying and improved glucose tolerance were confirmed in GLP-1R knockout mice. GCGR activity was confirmed by reduced plasma amino acids, increased hepatic expression of nicotinamide N-methyltransferase and increased energy expenditure. BI 456906 produced greater bodyweight reductions than maximally efficacious semaglutide doses and modulated gene expression, including genes involved in amino acid metabolism. BI 456906 is a potent dual agonist that produces bodyweight-lowering effects through both GLP-1R and GCGR agonism.

2022-12-09 | GSE211105 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data