Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Cell Atlas of Microbe-Responsive Processes in the Zebrafish Intestine

ABSTRACT: To understand intestinal cell-specific responses to host commensal bacteria, we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single-cell RNA-seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue, and describe distinct microbial responses in each cell type.

ORGANISM(S): Danio rerio

PROVIDER: GSE161855 | GEO | 2020/11/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A Cell Atlas of Microbe-Responsive Processes in the Zebrafish Intestine

Project description:A Cell Atlas of Microbe-Responsive Processes in the Zebrafish Intestine

| PRJNA679624 | ENA

Directed endocytosis mediates immune communication between an epithelial commensal microbe and the host

Project description:Commensal bacteria influence host physiology, including immune responses, without invading host tissues. We show that proteins from segmented filamentous bacteria (SFB), which are immunomodulatory commensal microbes, are transferred into intestinal epithelial cells by adhesion-directed endocytosis that is distinct from the clathrin-dependent endocytosis of invasive pathogens. SFB transfer microbial cell wall-associated proteins, including an antigen that stimulates mucosal Th17 cell differentiation, into the cytosol of epithelial cells. Removal of CDC42 activity in vivo led to disruption of endocytosis induced by SFB, decreased epithelial antigen acquisition with consequent loss of immune modulation by SFB-specific CD4 T cells and mucosal Th17 cells. Our findings indicate direct communication between a resident gut microbe and the host and show that intestinal epithelial cells acquire antigens from commensal bacteria for generation of T-cell responses to the resident microbiota.

2019-01-10 | GSE124848 | GEO

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

Project description: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.

2023-01-01 | E-MTAB-12215 | biostudies-arrayexpress

CITE-seq Analysis of Dendritic Cells in the Gut-Draining Lymph Node in anti-IL10R-treated mice with LIPSTIC Labeling of Akkermansia muciniphila Presenting Cells

Project description:Commensal-specific T cells contribute to tissue homeostasis within the intestines, and can influence disease pathology in the context of both cancer and autoimmunity. Antigen presenting cells play a critical role in influencing the differentiation of these T cells, but how the complex network of antigen presenting cells in the intestines drives commensal-specific T cells towards a variety of differentiation trajectories remains poorly understood. We examined the priming of T cells specific for the intestinal commensal bacterial species Akkermansia muciniphila, using the LIPSTIC system combined with single-cell RNA-sequencing to identify the APCs that prime A. muciniphila-specific T cells both at homeostasis when it elicits T follicular helper cells, and during inflammation, when it also elicits TH17 and TH1 cells. We found that A. muciniphila-specific T cells were primed by several transcriptionally distinct subpopulations of migratory cDC2s in both contexts. The identity of these subpopulations did not change with inflammation, but the distribution of presentation across the subpopulations shifted, with increased presentation by inflammatory cDC2s favoring TH1 and TH17 polarization. These results reveal how distinct T cell differentiation trajectories can be determined through varied interactions with multiple, functionally distinct subpopulations of APCs.

2026-01-05 | GSE313299 | GEO

CITE-seq Analysis of Dendritic Cells in the Gut-Draining Lymph Node at Homeostasis with LIPSTIC Labeling of Akkermansia muciniphila-Presenting Cells

2026-01-05 | GSE313298 | GEO

Expression data from mouse small intestinal γδ intraepithelial lymphocytes

Project description:The mammalian gastrointestinal tract harbors thousands of bacterial species that include symbionts as well as potential pathogens. The immune responses that limit access of these bacteria to underlying tissue remain poorly defined. In this study, we used microarrays to uncover the transcriptional responses that occur in small intestinal γδ intraepithelial lymphocytes following bacterial challenge. γδ intraepithelial lymphocytes (γδ IEL) were isolated by flow cytometry from the small intestines of germ-free mice, or from age- and sex-matched conventionally-raised counterparts. We extracted RNAs from these purified γδ IEL for analysis on Affymetrix DNA microarrays. The mice were all >8 weeks in age, and each sample represents a pool of RNAs from 5-8 mice.

2011-04-06 | E-GEOD-28437 | biostudies-arrayexpress

Single cell RNA sequencing of fetal mouse intestine at key stages of development (E13.5, E14.5, E15.5, E16 and E17.5)

Project description:Here, we present the fetal mouse intestine data from the project \\"Comparison of human and mouse mesenchyme identifies common and unique aspects of intestinal patterning\\". Whole intestines were harvested from fetuses from timed pregnant matings for wildtype C57BL/6 mice (Jax strain #000664). Fetal stages were confirmed according to the Theiler staging chart (https://www.emouseatlas.org/emap/ema/staging_criteria/staging_criteria.html). Whole intestines (from the common bile duct through the cecum) were collected at key stages of development (E13.5, E14.5, E15.5, E16 and E17.5). Male and female intestines from each stage were pooled and dissociated to single cells for single cell RNA sequencing as previously described (Miller et al. 2020 Dev Cell). Specifically, E13.5 was 6 intestines, E14.5 was 5 intestines, E15.5 was 4 intestines, E16 was 3 intestines and E17.5 was 3 intestines.

2024-04-01 | E-MTAB-13201 | biostudies-arrayexpress

Transcriptome Analysis of Developing Intestine [RNA-Seq]

Project description:Background: The muscularis externa (ME) of the adult intestine consists of two layers of visceral smooth muscle (VISM), the inner circular muscle (ICM) and outer longitudinal muscle (OLM), that form sequentially beginning at embryonic day (E) 13 and E15 in the developing mouse. Coordinated contraction of these two layers facilitates the movement of food down the digestive tract. Though abnormal ME function or development has been linked to pseudoobstruction and irritable bowel syndrome, little is known about the molecular character of the smooth muscle that comprises this tissue. We performed transcriptome analysis to identify genes that are enriched in intestinal mesenchyme tissue at E14.5, when the inner circular muscle (ICM) is well established. Results: Expression patterns of enriched mesenchyme genes were examined in publically available in situ databases, revealing over one hundred genes that are expressed in the ICM. Examination of the promoter regions for these genes revealed enrichment for cJUN transcription factor binding sites and cJUN itself was also enriched in ICM. A cJUN ChIP-seq at E14.5 showed that cJUN regulatory regions contained characteristics of muscle enhancers. E14.5 mouse intestines were harvested and grown for 24 hours in a transwell culture with or without Cyclopamine treatment. Separated epithelial and mesenchyme tissue populations or whole intestines were submitted for sequencing. Three replicates for each condition were collected.

2015-11-12 | E-GEOD-74920 | biostudies-arrayexpress

Transcription profiling of mouse HNF4 null small intestine

Project description:To define changes in gene expression resulting from loss of hnf4 in the small intestine. Experiment Overall Design: hnf4 null intestines were generated by breeding hnf4loxp mice to vill-cre mice. Animals appeared to be healthy. Gene arrays were performed on two null and two control intestines.

2008-06-12 | E-GEOD-3124 | biostudies-arrayexpress

microbiota regualtion of miRNA

Project description:This experiment was investigating how gut commensal bacteria and intestinal inflammation affect miRNA expression. We analyzed miRNA expression of spleen and intestine from specific pathogen free (SPF) B6 mice, germ-free (GF) B6 mice, and IL-10 knockout mice which have severe colitis by microarray. Thus we have total 6 samples: GF spleen; GF intestines; SPF spleen; SPF intestine; IL-10 KO spleen and IL-10 KO intestine. We directly isolated RNA from whole spleens or intestines without any treatments, and then did microarray analysis.

2011-11-23 | E-MEXP-3406 | 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