Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-species single-cell transcriptomic analysis reveals the landscape of animal gastric antrum [scRNA-Seq]

ABSTRACT: Purpose: To reveal the consistency and difference of gastric antrum epithelial cells among species and provides insights into the selection of model organisms in different research directions in the future. Methods:In this study, we collected antrum epithelial tissues from human, pig, rat and mouse for scRNA-seq and conducted cross species analysis. Results: In pig antral epithelium, we identify a novel cell cluster. We also discovered that the porcine antral epithelium owns stronger immune function than the other species. Further analysis reveals this may be due to the insufficient function of porcine immune cells. Conclusions:Our results replenish the information of multiple species of gastric antral epithelium at the single cell level, providing data resources for understanding the basic situation of gastric antrum epithelial cells.

ORGANISM(S): Rattus norvegicus Mus musculus Homo sapiens Sus scrofa

PROVIDER: GSE225275 | GEO | 2023/09/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cross-species single-cell transcriptomic analysis reveals the landscape of animal gastric antrum [RNA-Seq]

Project description:Purpose: One goal of the bulk RNA-seq of organoids is to verify the differentially expressed genes between species identified by scRNA-seq .The other goal is to detected the differentially expressed genes when organoids from different species were treated with TNFα Methods: The total RNA from organoids was extracted by RNeasy Mini Kit (Qiagen). After total RNA extraction and then subjected to high-throughput sequencing on an Illumina Novaseq 6000 platform. Results: Most of the differentially expressed genes between species identified by bulk RNA-seq are consistent with the genes filtered by scRNA-seq. Conclusions: F3 and CLCA1 show higher expression in organoids of pig antral epithelium than in other three species. TNFα treatment upregulated the expression of immune response genes in all species

2023-09-11 | GSE225274 | GEO

Healthy Antrum miRnome

Project description:A small RNA library of stomach antrum tissue was sequenced using high-throughput SOLiD sequencing technology. The study aims to provide complementary information of the role of miRNAs in molecular regulation process in the healthy human stomach, in order to establish a reference for future comparisons of altered miRNA expression due to the gastric tract diseases.

2014-03-26 | E-MTAB-2273 | biostudies-arrayexpress

Role of PDGFRA+ cells and a CD55+ PDGFRALo fraction in the gastric mesenchymal niche

Project description:PDGFRA-expressing mesenchyme supports intestinal stem cells. Stomach epithelia have related niche dependencies, but their enabling mesenchymal cell populations are unknown, in part because previous studies pooled the gastric antrum and corpus. Our high-resolution imaging, transcriptional profiling, and organoid assays identified regional subpopulations and supportive capacities of purified mouse corpus and antral PDGFRA+ cells. Sub-epithelial PDGFRAHi myofibroblasts are principal sources of BMP ligands and two molecularly distinct pools distribute asymmetrically along antral glands but together fail to support epithelial growth in vitro. In contrast, PDGFRALo CD55+ cells strategically positioned beneath gastric glands promote epithelial expansion in the absence of other cells or factors. This population encompasses a small fraction expressing the BMP antagonist Grem1. Although Grem1+ cell ablation in vivo impairs intestinal stem cells, gastric stem cells are spared, implying that CD55+ cell activity in epithelial self-renewal derives from other subpopulations. Our findings shed light on spatial, molecular, and functional organization of gastric mesenchyme and the spectrum of signaling sources for epithelial support.

2023-10-29 | GSE224737 | GEO

Gene expression changes in undifferentiated and differentiated human primary epithelial cells of antrum, corpus, and fundus

Project description:Gene expression changes specific for healthy undifferentiated and differentiated human gastric primary epithelial cells of different regions of the stomach were here determined in order to describe the transcriptomic profile of these cells in correlation to their DNA methylation pattern. In addition, gene expression changes upon 5-aza-2'-deoxycytidine treatment of antral gastric primary cells compared to mock-treated cells were deterimend.

2022-12-28 | GSE141657 | GEO

The genetic regulation of the gastric transcriptome is associated with metabolic and obesity-related traits and diseases

Project description:Tissue-specific gene expression and gene regulation lead to a better understanding of tissue-specific physiology and pathophysiology. We analyzed the transcriptome and genetic regulatory profiles of two distinct gastric sites, corpus and antrum, to identify tissue-specific gene expression and its regulation. The transcriptome data from corpus and antral mucosa highlights the heterogeneity of gene expression in the stomach. We identified enriched pathways revealing distinct and common physiological processes in gastric corpus and antrum. Physiological differences are mostly related to digestion and epithelial protection. Furthermore, we found an enrichment of the single nucleotide polymorphism (SNP)-based heritability of metabolic, obesity-related, and cardiovascular traits and diseases by considering corpus- and antrum-specifically expressed genes. In particular, we could prioritize gastric-specific candidate genes for multiple metabolic traits, like NQO1 which is involved in glucose metabolism, MUC1 which contributes to purine and protein metabolism or RAB27B being a regulator of weight and body composition.

2024-02-23 | GSE242339 | GEO

miRNA expression from gp130F/F mice antrum at 4 weeks of age

Project description:The molecular events promoting the initiation of gastric cancer (GC), the third most lethal cancer worldwide, are ill-defined. Here, we demonstrate that upregulation of miR-200 family members is associated with tumor initiation in the gp130F/F mouse model of early GC. The onset of gastric inflammation-associated adenomatous hyperplasia in gp130F/F mice occurs at ~6 weeks of age, with established intestinal-type tumors (3 months of age) progressively growing until a maximum size is reached at 6 months of age, with some evidence of carcinoma in situ. Since this phenotype histologically mimics early stage human GC, we therefore utilized gp130F/F mice as a model to identify miRNAs involved in the initiating molecular events leading to early stage GC. For this purpose, we performed miRNA microarrays on mouse gastric antrum tissue from gp130F/F and sex-matched littermate wild-type (gp130+/+) control mice aged 4 weeks; this age was chosen since antrum tissue from 4 week old (wo) gp130F/F mice is devoid of any histological signs of inflammation or hyperplasia, and is thus comparable to wild-type gastric antrum tissue

2017-12-01 | GSE93169 | GEO

Comprehensive Profiling of early Neoplastic Gastric Microen-vironment Modifications and Biodynamics in Impaired BMP-Signaling Foxl1+-Telocytes

Project description:FoxL1+telocytes (TCFoxL1+) are novel gastrointestinal subepithelial cells that form communication axis between the mesenchyme and epithelium. TCFoxL1+ are strategically positioned to be key contributors to the microenvironment through production and secretion of growth factors and extracellular matrix (ECM) proteins. In recent years, the alteration of the bone morphogenetic protein (BMP) signaling in TCFoxL1+ was demonstrated to trigger a toxic microenvironment with ECM remodeling that leads to the development of pre-neoplastic gastric lesions. However, a comprehensive analysis of variations in the ECM composition and its associated proteins in gas-tric neoplasia linked to TCFoxL1+ dysregulation has never been performed. This study provides a better understanding of how TCFoxL1+ defective BMP signaling participates in gastric pre-neoplastic microenvironment. Using a proteomic approach, we determined the changes in the complete matrisome of BmpR1a△FoxL1+ and control mice, both in total antrum as well as in isolated mesenchyme-enriched antrum fractions. Comparative proteomic analysis revealed that the deconstruction of the gastric antrum led to a more comprehensive analysis of the ECM frac-tion of gastric tissues microenvironment. These results show that TCFoxL1+ are key members of the mesenchymal cell population and actively participate in the establishment of the matrisomic fraction of the microenvironment; thus, influencing epithelial cell behavior

2023-03-11 | PXD038603 | Pride

Healthy Antrum miRnome

Project description:Healthy Antrum miRnome

| PRJEB5288 | ENA

Stromal cells from the murine stomach antrum - single cell RNA seq

Project description:The aim of the experiment is to characteirze the non-epithelial cells in the stomach antrum using single cell RNAseg

2023-09-09 | GSE148343 | GEO

Gene expression profiles of spontaneous gastric tumors in the antrum of the stomach of 30,60, and 90 day old CEA424-SV40 -T antigen transgenic mice.

Project description:Analysis of global gene expression in the antral portion of the stomach in control and mice with a developing tumor to get further insight into the exact tumor type and the influence of local gene expression. Total RNA obtained from tissue samples from the antrum. Follow up of gene expression over the time of the tumor development

2012-08-01 | E-GEOD-27711 | biostudies-arrayexpress

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