Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of transcriptional profiles of cultured intestinal ILC3s to freshly isolated splenic and intestinal ILC3s

ABSTRACT: Comparison of transcriptional profiles of cultured intestinal ILC3s to freshly isolated splenic and intestinal ILC3s

PROVIDER: PRJNA472472 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7194820.fastq.gz	Fastqsanger.gz
	SRR7194821.fastq.gz	Fastqsanger.gz
	SRR7194822.fastq.gz	Fastqsanger.gz
	SRR7194823.fastq.gz	Fastqsanger.gz
	SRR7194814.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 13

Similar Datasets

Comparison of transcriptional profiles of cultured intestinal ILC3s to freshly isolated splenic and intestinal ILC3s

Project description:ILC3s from the spleen (SP) and small intestine (SI) have been shown to be phenotypically and functional different. Intestinal factors are likely to regulate transcriptional profiles and thereby function of ILC3s. The goal of this study is to analyze if SI ILC3s acquire a SP-similar transcriptional profile after in vitro culture. Therefore transcriptional profiles of cultured SI ILC3s were compared to freshly isolated ILC3s of the murine SP and the SI by RNA seq technology. Cell suspension were generated from both organs and ILC3s (CD117+, Thy1.2+, KLRG1-, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1)) were sort purified. SI ILC3 were cultured for 7 days in vitro with IL-2, IL-7 and SCF. RNA was isolated and RNA sequencing was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological replicates. We show that intestinal ILC3 acquire a splenic-similar transcriptional profile after in vitro culture.

2020-03-17 | GSE114750 | GEO

Bulk RNA sequencing of NCR- ILC3s from the murine spleen and the small intestine

Project description:Splenic and intestinal NCR- ILC3s have been shown to be phenotypically and functional different. The goal of this study is to compare transcriptional profiles of NCR- ILC3s isolated of the murine spleen (SP) and the small intestine (SI) by RNA seq technology. Cell suspension were generated from both organs and NCR- ILC3s (CD117+, Thy1.2+, eYFP+, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1, NKp46)) were sort purified. RNA was isolated and RNA sequencing was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological triplicates. We provide the first comparison of transcriptional profiles of intestinal and splenic NCR- ILC3s.

2020-03-17 | GSE114749 | GEO

Comparison of transcriptional profiles of (1) intestinal ILC3s isolated from WT and IL-17D-deficient mice; (2) CD93+ILC3s and CD93-ILC3s from WT mice

Project description:IL-17D/CD93 axis was essential for ILC3s hemostasis. In order to further understand how IL-17D-CD93 axis regulate ILC3s function, we conducted RNA-seq analysis of ILC3s.

2021-05-20 | GSE165788 | GEO

Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [ATAC-seq]

Project description:To determine the molecular regulation of ILC3s by Brg1, small intestinal ILC3s (Lin-Thy1highCD45low) from Brg1-deficient and control ILC3s were subjected to assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq).

2020-07-01 | GSE148078 | GEO

Microarray data from human cultured ILC3s

Project description:Innate lymphoid cells (ILCs) are tissue-resident lymphocytes subdivided into ILC1s, ILC2s and ILC3s based on core regulatory programs and signature cytokines secreted. ILCs exhibit functional plasticity: for instance, human IL-22-producing ILC3s convert into IFN-γ-producing ILC1-like in vitro. Whether this conversion occurs in vivo is unclear. Using flow cytometry, mass cytometry and scRNAseq, here we found that ILC3s and ILC1s occupy opposite ends of a spectrum including discrete subsets in human tonsils. RNA velocity suggested strong directionality toward ILC1s for one ILC3-ILC1 intermediate cluster. Clonal analysis revealed graded ability of ILC3-ILC1 subsets to convert into ILC1-like cells. When examined in humanized mice, ILC3 acquisition of ILC1 features showed tissue-dependency. In chromatin studies, Aiolos emerged as a nuclear factor that cooperates with Tbet to repress evolutionarily conserved regulatory elements active in ILC3s. The human intestine also exhibited an ILC3–ILC1 transitional population. We conclude that conversion of ILC3s to ILC1-like occurs in vivo in human tissues, and that tissue factors and Aiolos are crucial for this process.

2019-06-18 | GSE132843 | GEO

Chromatin accessibility landscapes of intestinal WT Nkp46-CC6- ILC3 (Double Negative, DN ILC3) and BATF-deficient cKO DN ILC3s sorted from intestine

Project description:Group 3 innate lymphoid cells (ILC3s) are crucial for the maintenance of host-microbiota homeostasis in gastrointestinal mucosal tissues. The mechanisms that maintain lineage identity of intestinal ILC3s, and ILC3s-mediated orchestration of microbiota and mucosal T cell immunity are elusive. Here, we identified BATF as a gatekeeper of ILC3s homeostasis in the gut. Depletion of BATF in ILC3s resulted in excessive interferon-γ production, dysbiosis, aberrant T cell immune responses and spontaneous inflammatory bowel disease (IBD), which was considerably ameliorated by removal of adaptive immunity or antibiotic treatment. Mechanistically, BATF directly regulates ILC3s identity by globally shapes chromatin landscape of ILC3s. BATF directly binds to the cis-regulatory elements of type 1 effector genes, restrains their chromatin accessibility and inhibits their expression. Conversely, BATF promotes chromatin accessibility of genes involved in MHCII antigen processing and presentation pathways. Collectively, our findings reveal BATF is a promising candidate to maintain ILC3s stability and coordinate ILC3s–mediated control of intestinal homeostasis.

2022-09-08 | GSE212590 | GEO

Intestinal ILC3s migrate to the kidney and promote renal fibrosis via PD-1-mediated activation

Project description:Group 3 innate lymphoid cells (ILC3s) are enriched in mucosae, regulating inflammation and tissue repair, yet their role in renal fibrosis remains unclear. Here, we reported that renal fibrosis and dysfunction were associated with increased ILC3s in human kidney and blood. Using murine models, we showed that the rapid accumulated ILC3s in the kidney primarily originated from the intestinal mucosa. By performing scRNA-seq of ILC(3)s in kidneys and small intestines at different stage of renal fibrosis, we revealed the characteristic and migratory mechanism of these cells. Within the fibrotic kidney, ILC3s upregulated PD-1 to directly activate myofibroblasts and facilitate fibrotic niche formation by producing IL-17A. We also isolated ILCs from Pdcd1-knockout-UUO3d kidneys to gain the molecular mechanism of how PD-1 influence ILC3s' pro-fibrogenic effect. Collectively, we reveal a hitherto unrecognized migration pathway of ILC3s from the intestine to the kidney and the PD-1-dependent function of ILC3s in promoting renal fibrosis.

2024-05-29 | GSE249724 | GEO

Gene expression data for MACS-isolated primary splenic T cells

Project description:We are interested in unveiling potential gene expression alterations underlying the T cell-related phenotypes observed in DUSP4-/- mice. We used microarray to obtain a macroscopic views of gene profiles comparing freshly isolated splenic T cells from WT and DUSP4-/- mice

2016-02-25 | GSE75319 | GEO

Comparison of transcriptional profiles of (1) intestinal ILC3s isolated from WT and IL-17D-deficient mice (2) CD93+ILC3s and CD93-ILC3s from WT mice

Project description:Comparison of transcriptional profiles of (1) intestinal ILC3s isolated from WT and IL-17D-deficient mice (2) CD93+ILC3s and CD93-ILC3s from WT mice

| PRJNA697917 | ENA

Functional Targeting of ILC2s and ILC3s reveals selective roles in intestinal fibrosis and homeostasis.

Project description:Innate lymphoid cells (ILCs) are long-lived tissue-resident analogues to T helper cell subsets that lack antigen-specific receptors. Understanding the roles of specific ILC subsets in chronic inflammation and fibrosis has been hampered by a lack of adequate tools for their selective targeting. Here, we used two Cre-deleter strains, Il17rb-CreERT2-eGFP and Rorc-Cre, to selectively delete RORa, a master transcriptional regulator, in ILC2s and ILC3/Th17 cells, respectively. Deletion of RORa in ILC2s led to a significant loss of gastrointestinal ILC2s, a concomitant increase in ILC3s, elevated Th17-type responses, and heightened susceptibility to Crohn’s-like fibrosis in a Salmonella infection model. In contrast, RORa deletion in ILC3/Th17 cells reduced IL-17 production, protecting against fibrosis. We further confirmed the role of IL-17 and ILC3 in fibrotic responses using isolithocholic acid (isoLCA), a microbially-derived secondary bile acid and RORγt inverse agonist. In RORγt reporter and Th17-deficient Rag1−/− mice, isoLCA reduced IL-17 production by ILC3s. In the context of intestinal fibrosis, we show that isoLCA attenuates collagen deposition and fibrotic pathology by dampening RORγt-dependent IL-17 production by ILC3s. These findings reveal a novel interplay between ILC2s and ILC3s in gut homeostasis and demonstrate the therapeutic potential of targeting RORγt in ILC3s as a strategy for preventing fibrosis.

2025-05-15 | GSE290467 | 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