Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Culture associated DNA methylation changes impact on cellular function of Human Intestinal Organoids (Expression)

ABSTRACT: Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration, proinflammatory cytokine stimulation and differentiation on organoid DNA methylation. The experiment consists of RNA-seq of intestinal organoid cultures from paediatric ileum and colon.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Rachel Edgar

PROVIDER: E-MTAB-11548 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Culture associated DNA methylation changes impact on cellular function of Human Intestinal Organoids (Methylation)

Project description:Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration, proinflammatory cytokine stimulation and differentiation on organoid DNA methylation. The experiment consists of genome-wide DNA methylation profiling by Infinium HumanMethylationEPIC BeadChip of intestinal organoid cultures from paediatric ileum and colon. Our genome wide DNA methylation datasets represent a unique resource, which can be used by other researchers to validate their model systems.

2022-08-31 | E-MTAB-11545 | biostudies-arrayexpress

DNA methylation array of human intestinal organoids derived from paediatric small and large intestine

Project description:Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration on organoid DNA methylation. The experiment consists of genome-wide DNA methylation profiling by Infinium HumanMethylationEPIC BeadChip of intestinal organoid cultures from paediatric ileum and colon. Our genome wide DNA methylation datasets represent a unique resource, which can be used by other researchers to validate their model systems Note: Some samples in this data set were replicated from a previously submitted to ArrayExpress under accession number E-MTAB-4957. They're clearly marked in the “Description” field in sample annotations.

2022-08-31 | E-MTAB-9748 | biostudies-arrayexpress

The genetic basis for differential macrophage activation

Project description:Differential macrophage activation mediate genetic differences to a variety of inflammatory pathologies. We wanted to elucidate the transcriptional and regulatory programs regulating differential macrophage activation in genetically diverse mouse strains. Bone marrow-derived macrophages (BMDMs) from AJ and C57BL/6j mice were left unstimulated, stimulated with IFN/TNF, or IL-4, or CpG, or LPS or IFN/TNF and infected with a type II (Pru A7) strain of Toxoplasma gondii, or infected with Pru A7 and gene expression analyzed 18 hrs later.

2013-05-18 | E-GEOD-47046 | biostudies-arrayexpress

RNA-sequencing of coding RNA from human purified intestinal epithelial samples and organoids derived from foetal and paediatric small and large intestine

Project description:Human intestinal epithelial organoids (IEO) culture models are rapidly emerging as novel experimental tools to investigate fundamental aspects of intestinal epithelial (patho)physiology. Cellular source and culture protocols vary between different IEO models and reliable markers for their characterization/validation are currently limited. Here, we provide the following reference datasets of transcriptomic profiling by RNA-sequencing: Purified intestinal epithelial cells (EpCAM+) from paediatric ileum and colon, Intestinal organoid cultures from paediatric ileum and colon, Purified intestinal epithelial cells (EpCAM+) from foetal small intestine and foetal large intestine, Intestinal organoid cultures from foetal small intestine and foetal large intestine, Intestinal organoid cultures derived from induced pluripotent stem cells.<br> Complementary data from methylation profiling on the same samples have been deposited at ArrayExpress under accession number E-MTAB-4957 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4957 ).</br>

2018-01-20 | E-MTAB-5015 | biostudies-arrayexpress

Expression Data from Allogeneic Human Mesenchymal Stem Cells and Primary Cultures of Human Alveolar Epithelial Type II Cells

Project description:Acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) is a severe syndrome affecting more than 200,000 patients annually in the U.S. New studies are needed to understand the biological and clinical mechanisms that impair alveolar epithelial function. Also, innovative therapies are needed for the resolution of pulmonary edema in ARDS. We and other investigators have reported that bone marrow derived mesenchymal stem cells (MSCs) are effective in preclinical models of ALI due to their ability to secrete several paracrine factors that can regulate lung endothelial and epithelial permeability, including growth factors, anti-inflammatory cytokines, and antimicrobial peptides. So in this study we will test the therapeutic value of human MSCs in an in vitro model of acute lung injury induced by pro-inflammatory cytokines. We will identify differentially expressed genes in primary cultures of human alveolar epithelial type II cells and human bone marrow derived mesenchymal stem cells using Affymetrix gene expression arrays. Human mesenchymal stem cells (MSCs) and human alveolar epithelial type II cells were co-cultured in a transwell system. The cells were stimulated with cytomix (a combination of different pro-inflammatory cytokines) under different conditions. Cells were harvested for Affymetrix gene expression arrays. Total 25 samples are analyzed, 3~5 replicates are included.

2015-07-08 | E-GEOD-68610 | biostudies-arrayexpress

RNA-sequencing of human induced pluripotent stem cell-derived intestinal epithelial organoids

Project description:The purpose of this study was to characterise iPSC-derived human intestinal epithelial organoids (iPSCo) by comparing these cultures with primary purified intestinal epithelial cells (IEC). Intestinal epithelial organoid (IEO) cultures were derived from at least three different lines of iPSCs, RNA was extracted and gene expression was profiled using RNA-sequencing. We compared these profiles with datasets we have previously derived from purified IEC from mature terminal ileum (TI) and sigmoid colon (SC) as well as human fetal proximal gut (FPG) and fetal distal gut (FDG).

2018-10-22 | E-MTAB-7306 | biostudies-arrayexpress

RNA-seq of human intestinal organoids co-cultured with human PMNs infected with Salmonella enterica serovar Typhimurium and Enteritidis at 8h post infection

Project description:The purpose of this experiment was to identify the contribution of PMNs in intestinal epithelial responses to Salmonella infection.

2022-12-02 | E-MTAB-11089 | biostudies-arrayexpress

DNA-methylation profiling of human induced pluripotent stem cell -derived intestinal epithelial organoids

Project description:The purpose of this study was to characterise iPSC-derived human intestinal epithelial organoids (iPSCo) by comparing these cultures with primary purified intestinal epithelial cells (IEC). Intestinal epithelial organoid (IEO) cultures were derived from at least three different lines of iPSCs, DNA was extracted and gene expression was profiled using Illumina Infinium HumanMethylation450Beadarray. We compared these profiles with datasets we have previously derived from purified IEC from mature terminal ileum (TI) and sigmoid colon (SC) as well as human fetal proximal gut (FPG) and fetal distal gut (FDG).

2018-10-23 | E-MTAB-7289 | biostudies-arrayexpress

RNA-seq of human intestinal organoids infected with Salmonella enterica at 2.5h and 8h post infection

Project description:The purpose of this experiment was to identify intestinal epithelial responses to various strains of Salmonella enterica. Human intestinal organoids were infected with three serovars of Salmonella; Typhimurium, Enteritidis and Typhi, as well as type 3 secretion system -1 and -2 mutants in Typhimurium in order to identify host responses that were similar and unique to each serovar, and responses that were dependent on these secretion systems.

2021-10-01 | E-MTAB-10451 | biostudies-arrayexpress

Epithelial maturation of human intestinal organoids from pluripotency entirely in vitro

Project description:In vitro human pluripotent stem cell derived intestinal organoids (HIOs) are immature and lack for diverse differentiated secretory cell types. We would like to test the hypothesis whether addition of a mesenchyme secreting ligand which is depleted in canonical organoid culture media could increase the maturity and secretory cell type diversity in HIOs in vitro. To do this, we adapted the directed differentiation protocol of HIOs by growing HIOs in media with EGF, NOGGIN, R-spondin-1 (ENR) for 30 days, isolated epithelial cells with dispase, recovered them with adult intestinal enteroid media with Wnt-3A (WENR). Then we introduced the mesenchyme secreting ligand NRG1 to the established enteroid culture (WENR+NRG1) and compared them to the enteroids grown in control condition (WENR).

2022-12-31 | E-MTAB-10876 | 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