Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell resolution of the adult zebrafish intestine under conventional conditions, and in response to an acute, natural infection

ABSTRACT: Single cell resolution of the adult zebrafish intestine under conventional conditions, and in response to an acute, natural infection

PROVIDER: PRJNA957280 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Single cell resolution of the adult zebrafish intestine under conventional conditions, and in response to an acute, natural infection

Project description:We used single cell RNA sequencing to analyze the diversity of intestinal cells under conventional conditions and the effect of an acute, natural Vibrio cholerae infection on the intestinal transcriptome.

2023-07-25 | GSE230044 | GEO

Transcriptional profiling of murine small intestine in conventional or SPF housing conditions

Project description:We studied the influence of the microbiota on intestinal homeostasis and tumor development after loss of the intestinal tumor phenotype in Msh2-Lynch mice upon rederivation of the mouse line in an SPF facility. We generated RNA seq data from total RNA of small intestine (jejunum) derived from either conventional or SPF mice.

2022-02-08 | GSE171996 | GEO

Transcriptional profiling of murine small intestine in conventional or SPF housing conditions

Project description:Transcriptional profiling of murine small intestine in conventional or SPF housing conditions

| PRJNA721667 | ENA

Zebrafish intestine

Project description:Zebrafish intestine Raw sequence reads

| PRJNA989424 | ENA

Comparison of gene expression in conventional and germ-free intestine

Project description:Comparison of gene expression in conventional and germ-free intestine

| PRJNA92817 | ENA

Genome-wide transcriptome profiling of Colon Intestine-Chip and Conventional Organoid Cell Culture System Using RNA-seq

Project description:goal of this study was A) to compare global RNA-sequencing (RNA-seq) profiles data of organoid- derived colonic epithelial cells cultured and differentiated in i) conventional suspension organoids cultures (n=3), ii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and stretch (n=4), iii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and with stretch (n=4), iv) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and without stretch (n=4), v) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and stretch (n=6), vi) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and stretch (n=4), vii) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and with stretch (n=4), viii) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and without stretch (n=4), ix) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and stretch (n=3), and B) to identify differences in transcriptome profiles of organoid- derived colonic epithelial cells between following two conditions, unstimulated and basolaterally stimulated with IL-22 (10pM, 100pM or 1nM) Colon Intestine-Chips.

2021-11-10 | GSE179130 | GEO

The complex pattern of epigenomic variation between natural yeast strains at single-nucleosome resolution

Project description:We investigated natural inter-individual variation of the epigenome in a quantitative manner. To probe the degree of natural epigenomic diversity in S. cerevisiae, we compared three unrelated wild strains using replicated Mnase-seq and ChIP-seq profiling at mononucleosomal resolution for five histone marks (H3K4me3, H3K9ac, H3K14ac and H4K12ac and H3K4me1).

2015-07-21 | E-MTAB-3390 | biostudies-arrayexpress

Molecular basis of flowering under natural long-day conditions in Arabidopsis

Project description:Plants sense light and temperature changes to regulate flowering time. The expression of the florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the lab. Providing our lab growth conditions with a red/far-red light ratio similar to open field conditions and average natural temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Here, we use RNA-seq to identify and understand the molecular differences between natural growth conditions, conventional lab growth conditions, and supplemented lab growth conditions that mimic natural conditions. Non-NIH grant(s): Grant ID: NSF 1656076 Grant title: Exploring Seasonal Flowering Mechanisms Affiliation: University of Washington Name: Takato Imaizumi

2018-04-01 | GSE110605 | GEO

Acetylome Analysis of Feline Small Intestine Following Toxoplasma gondii Infection

Project description:Toxoplasma gondii threats to the health of one-third of the world's population. Cat is the natural definite host of T. gondii. However, the biological changes of feline small intestine following T. gondii infection remains mysterious event. Protein acetylation modification which is a dynamic and reversible post-translational modification (PTM) plays important roles in regulating various physiological functions. In this study, we used affinity enrichment and high resolution LC-MS/MS to analyze the alteration of acetylation event in feline small intestine infected by Prugniuad (Pru) strain of Toxoplasma gondii.

2020-07-09 | PXD018799 |

Gene expression profiling of small intestine (SI) NKp46+RORgt+ and NKp46+RORgt- Innate Lymphoid Cells (ILCs)

Project description:The aim of this study was to analyze the global transcriptional profiles of small intestine (SI) Innate Lymphoid Cells (ILCs) expressing the NK cell marker NKp46. Based on differential expression of the RORgt transcription factor SI NKp46+ ILCs can be divided in NKp46+RORgt- and NKp46+RORgt+ cells. While NKp46+RORgt- cells produce IFN-g, like conventional Natural Killer (NK) cells, NKp46+RORgt+ cells secrete IL-22, like Lymphoid Tissue inducer (LTi) cells. We compared the global transcriptional profiles of both NKp46+RORgt- and NKp46+RORgt+ cells to conventional splenic NK cells and to SI NKp46-RORgt+ cells, which contain adult LTi cells. By following this approach, we showed that SI NKp46+RORγt- ILCs correspond to SI NK cells. We also identified a transcriptional program conserved in adult SI NKp46+RORγt+, NKp46-RORγt+ ILCs and fetal LTi. The various ILC cell populations analyzed in this study were isolated from C57BL/6 RORc(gt)+/GFP reporter mice. SI NKp46+RORγt- (NKp46+GFP-) cells, SI NKp46+RORγt+ cells (NKp46+GFPlow and NKp46+GFPhigh cells) and NKp46-RORγt+ ILCs, including adult LTi cells , were sorted by flow cytometry from CD3- lamina propria cells of small intestine (SI) of RORc(γt)+/GFP reporter mice . Splenic NKp46+RORγt- (NKp46+GFP-) cells were also sorted as the reference for conventional NK cells. Two replicates of each populations were produced and analyzed.

2011-06-20 | E-GEOD-29777 | 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