Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Distinct microbial and immune niches of the human colon

ABSTRACT: Gastrointestinal microbiota and immune cells interact closely and display regional specificity, but little is known about how these communities change with location.

PROVIDER: PRJEB32887 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3354240_1.fastq.gz	Fastqsanger.gz
	ERR3354240_2.fastq.gz	Fastqsanger.gz
	ERR3354290_1.fastq.gz	Fastqsanger.gz
	ERR3354290_2.fastq.gz	Fastqsanger.gz
	ERR3354241_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 164

Similar Datasets

Transcriptional responses of human colon and liver cancer cells to TCF inhibition.

Project description:Dysregulation of Wnt/TCF signaling is closely associated with cancers arising from the gastrointestinal tract, inlcluding colon cancer and liver cancer. The goal of this study is to understand the transcriptional programs underlying Wnt/TCF activation in gastrointestinal cancers. We examined the transcriptional responses to TCF inhibition in cultured human colon cancer cells and liver cancer cells that are characteristic of Wnt pathway activation.

2013-08-01 | GSE46465 | GEO

Transcriptional responses of human colon and liver cancer cells to TCF inhibition.

2013-08-01 | E-GEOD-46465 | biostudies-arrayexpress

Global acetylation profiling for multiple Arabidopsis thaliana plastid N-terminal acetyltransferases

Project description:Protein acetylation is a universally conserved modification occurring on N-termini (N-Terminal acetylation, NTA). Although recent reports indicate that NTA occur frequently in plant plastids, little is known about the machinery involved in plastid acetylation and why these modifications are that frequent in this organelle. Searches for new putative N-acetyltransferase genes in Arabidopsis thaliana highlighted eight putative candidates located at plastid subcellular location. In this study, we investigated the N-acetyltransferase specificity of these enzymes using the global acetylome profiling test (GAP test).

2020-07-13 | PXD016205 | Pride

Distinct microbial and immune niches of the human colon.

Project description:Gastrointestinal microbiota and immune cells interact closely and display regional specificity; however, little is known about how these communities differ with location. Here, we simultaneously assess microbiota and single immune cells across the healthy, adult human colon, with paired characterization of immune cells in the mesenteric lymph nodes, to delineate colonic immune niches at steady state. We describe distinct helper T cell activation and migration profiles along the colon and characterize the transcriptional adaptation trajectory of regulatory T cells between lymphoid tissue and colon. Finally, we show increasing B cell accumulation, clonal expansion and mutational frequency from the cecum to the sigmoid colon and link this to the increasing number of reactive bacterial species.

| S-EPMC7212050 | biostudies-literature

Transcriptional cofactors display core promoter class-specificity

Project description:Transcriptional cofactors display core promoter class-specificity

| PRJNA477764 | ENA

Substrate profiling of the metalloproteinase ovastacin – Implications for its physiological function in mammalian fertilization

Project description:The metalloproteinase ovastacin is released by the mammalian oocyte upon fertilization and cleaves zona pellucida protein 2, a component of the surrounding extracellular matrix, at a distinct cleavage site. This limited proteolysis hardens the zona pellucida, abolishes sperm binding and thereby regulates fertility. Therefore, this process has to be tightly controlled by the plasma protein fetuin-B, an endogenous competitive inhibitor. At present, little is known about how the cleavage characteristics of ovastacin differ from closely related proteases. Physiological implications of ovastacin beyond ZP2 cleavage are still obscure. In this study, we employed N-terminal amine isotopic labeling of substrates (N-TAILS) contained in the secretome of mouse embryonic fibroblasts to elucidate the substrate specificity and the precise cleavage site specificity. Furthermore, we were able to unravel the physicochemical properties governing enzyme-substrate interactions. Eventually, we identified several potential physiological substrates with significance for mammalian fertilization. These results suggest that ovastacin might affect sperm interaction beyond zona pellucida hardening

2023-09-15 | PXD038561 | JPOST Repository

Transcriptional profiles of embryonic stem cell derived gastrointestinal tissue.

Project description:Successful differentiation methods have been developed in several endodermal organs, including liver, pancreas, and intestine from embryonic stem cell and induced pluripotent stem cells. Compare to these organs, however, little has been known in gastric differentiation from embryonic stem cells. Here, we established a method of gastrointestinal tissue differentiation methods, including stomach regions from embryonic stem cells. These gastrointestinal tissue built gut primordium-like spheroids, which is also able to mature into adult tissue containing all differentiated cells in three-dimensional culture. These embryonic stem cells derived gastrointestinal tissue possessed the similar gene expression profile that of adult stomach. These data indicated that functional gastrointestinal tissue can be derived from embryonic stem cells by mimicking in vivo development and could be useful for investigating gastrointestinal study such as disease modeling.

2015-07-20 | GSE60031 | GEO

Global profiling of acetylation reveals a new family with dual-specific lysine and N-terminal acetyltransferase activity in the plastids of Arabidopsis

Project description:Protein acetylation is a universally conserved modification occurring on N-termini (N--acetylation, NTA) and on internal lysines residues (-lysine-acetylation, KA). So far, NTA and KA were known to be supported by distinct families of enzymes (NATs and KATs, respectively), despite most of them share a common GCN5-related N-acetyltransferase (GNAT) domain. Although recent reports indicate that both NTA and KA occur frequently in plant plastids, little is known about the machinery involved in plastid acetylations and why these modifications are that frequent in this organelle. Searches for new putative NAT and KAT genes in Arabidopsis thaliana illuminate a common pool of ten putative candidates, displaying a number of unique features both at the level of conserved key residues and motifs. Here, we show that eight out of the ten candidates are associated with the plastids. In vivo investigation based on global quantitative mass spectrometry of these enzymes revealed that they exhibit a number of unique features, supporting both NAT and KAT activities of the plastids. All identified enzymes show distinct KAT substrate specificity and display unexpected relaxed NAT substrate specificity, each with differences in terms of NTA yields and preferred substrates. Together, this study reveals an unexpected multitasking protein modification machinery dedicated to the plastids of plant. We suggest that this machinery likely evolved to support specific needs of this organelle.

2020-07-07 | PXD015875 | JPOST Repository

Transcriptional cofactors display core promoter class-specificity in human

Project description:Transcriptional cofactors display core promoter class-specificity in human

| PRJNA521352 | ENA

Characterization of Human Bone Marrow Niches with Metabolome and Transcriptome Profiling

Project description:The hematopoietic niches in bone marrow (BM) are specialized compartments working in harmony to regulate all the steps of the hematopoiesis cascade. Little is known about how BM niches in healthy humans. Therefore, we investigated the presence of different niches in healthy human BM using comparative omic technologies (Metabolomic and transcriptomic). We sequenced and comparative analyzed mRNA samples of human bone marrow mesenchymal stem cells (MSCs) to generate the gene expression profiles of these cells which obtained from two anatomically different BM regions (R1 and R2).

2021-03-01 | GSE145008 | 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