Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Vitamin D Receptor binding and chromatin accessibility in mouse duodenal crypt and villus and colon epithelium

ABSTRACT: VDR is critical for Ca++ homeostasis. While its role in this process within the intestine has primarily been focused to the duodenal epithelium, we have uncovered a compensatory role for VDR in the colon in mediating Ca++ uptake. Here, we compare VDR genomic binding properties in the colon and duodenum using ChIP-seq. We also examine the chromatin accessibility between these intestinal regions.

ORGANISM(S): Mus musculus

PROVIDER: GSE161038 | GEO | 2023/11/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide transcriptome profiling of human duodenal organoids, Duodenum Intestine-Chip and adult duodenal tissue using RNA-seq.

Project description:The goal of this study was to compare global RNA expression data obtained from: i) duodenal organoids cultured in conventional plastic-adherent Matrigel drop overlaid with growth medium; ii) Duodenum Intestine-Chips derived from organoids in the presence of constant flow and stretch; iii) human adult duodenum tissue and to verify whether Duodenum Intestine-Chip faithfully recapitulates human adult duodenum tissue and to better understand how much it differs from the organoids from which it’s derived.

2020-01-06 | GSE135196 | GEO

Apolipoprotein A4 Defines the Villus-Crypt Border in Duodenal Specimens for Celiac Disease Morphometry.

Project description:Histological evaluation of the small intestinal mucosa is the cornerstone of celiac disease diagnostics and an important outcome in scientific studies. Gluten-dependent injury can be evaluated either with quantitative morphometry or grouped classifications. A drawback of mucosal readings is the subjective assessment of the border where the crypt epithelium changes to the differentiated villus epithelium. We studied potential immunohistochemical markers for the detection of the villus-crypt border: apolipoprotein A4 (APOA4), Ki-67, glucose transporter 2, keratin 20, cytochrome P450 3A4 and intestinal fatty-acid binding protein. Among these, villus-specific APOA4 was chosen as the best candidate for further studies. Hematoxylin-eosin (H&E)- and APOA4 stained duodenal biopsy specimens from 74 adult patients were evaluated by five observers to determine the villus-to-crypt ratio (VH : CrD). APOA4 delineated the villus to crypt epithelium transition clearly, and the correlation coefficient of VH : CrD values between APOA4 and H&E was excellent (r=0.962). The VH : CrD values were lower in APOA4 staining (p<0.001) and a conversion factor of 0.2 in VH : CrD measurements was observed to make the two methods comparable to each other. In the intraobserver analysis, the doubled standard deviations, representing the error ranges, were 0.528 for H&E and 0.388 for APOA4 staining, and the ICCs were 0.980 and 0.971, respectively. In the interobserver analysis, the average error ranges were 1.017 for H&E and 0.847 for APOA4 staining, and the ICCs were better for APOA4 than for H&E staining in all analyses. In conclusion, the reliability and reproducibility of morphometrical VH : CrD readings are improved with the use of APOA4 staining.

| S-EPMC8358775 | biostudies-literature

Differential gene expression in Lrig1null duodenal tumors compared to normal duodenum

Project description:Leucine-rich repeats and immunoglobulin-like domains 1 (Lrig1) is a pan-ErbB negative regulator and intestinal stem cell marker downregulated in many malignancies. Over 91% Lrig1-CreERT2/CreERT2 (Lrig1-/-) mice developed duodenal adenomas, providing the first in vivo evidence Lrig1 acts as a tumor suppressor. We thus characterize the differential expressing transcripts in these duodenal adenomas to explore the pathegenesis. Elevated expression of the Egfr ligands was detected in adenomas compared to adjacent normal tissue. These adenomas also expressed the gastric-specific genes Gastrokine1 and Mucin5ac, indicating gastric metaplasia. In this dataset, we include the expression data obtained from proximal adenomas as well as adjacent normal tissue and wildtype proximal duodenum. These data are used to obtain 679 upregulated and 874 downregulated transcripts in tumors. Total RNA from matched duodenal tumors or adjacent normal or wildtype duodenum was isolated with Rneasy (with Dnase digestion) and used to probe the Affymetrix Mouse Gene 1.0 ST chip; the probe was prepared with Ambion Expression Target preparation Kit P/N 4411974.

2015-01-04 | E-GEOD-64640 | biostudies-arrayexpress

Gene expression in duodenal biopsy samples from CVID enteropathy patients and healthy controls

Project description:A subgroup of CVID patients presents with gastrointestinal complications (enteropathy), which manifests in the duodenum as celiac like-diese ase. CVID enteropathy patients can present with severe histopathology in form of villous atrophy (CVID VA) or without VA (CVID noVA). RNAseq data from CVID VA and CVID noVA derived duodenal tissues were compared to each other and to healthy controls.

2023-02-10 | GSE189820 | GEO

Differential gene expression in Lrig1null duodenal tumors compared to normal duodenum

2015-01-04 | GSE64640 | GEO

Gene expression profiles in human duodenal organoid-derived monolayer

Project description:The human small intestine is the key organ for absorption, metabolism, and excretion of orally administered drugs. To preclinically predict these reactions in drug discovery research, a cell model that can precisely recapitulate the in vivo human intestinal monolayer is desired. Here, we developed a monolayer platform using human biopsy-derived duodenal organoids for application to pharmacokinetic studies. The human duodenal organoid-derived monolayer was prepared by a simple method in 3–8 days. It consisted of polarized absorptive cells and had a barrier function. It showed much higher cytochrome P450 (CYP) 3A4 and carboxylesterase (CES) 2 activities than Caco-2 cells. It also showed efflux activity of P-glycoprotein (P-gp) and inducibility of CYP3A4. Finally, its gene expression profile was closer to the adult human duodenum, compared to the profile of Caco-2 cells. Based on these findings, this monolayer assay system using biopsy-derived human intestinal organoids is likely to be widely adopted.

2021-05-19 | GSE160695 | GEO

Transcription profiling of human duodenal mucosa samples taken from subjects after ingesting a Lactobacillus plantarum WCFS1 supplement for two weeks

Project description:The effects of a 2-week suppletion period with L. plantarum WCFS1 on duodenal gene expression profiles was investigated in healthy subjects in a placebo-controlled doouble-blind study. Each subject ingested a supplement containing L. Plantarum WCFS1 once a day. After that period, tissue samples from the horizontal part of the duodenum were obtained by standard flexible gastroduodenoscopy, and Affymetrix microarrays were used to determine genome-wide gene expression profiles.

2008-11-14 | E-MEXP-1336 | biostudies-arrayexpress

Endoscopic Placement of Metal Stents in Treating Patients With Cancer- Related Duodenal Obstruction

Project description:RATIONALE: The use of endoscopy to place metal stents in the duodenum is less invasive than surgery for treating cancer-related duodenal obstruction and may have fewer side effects and improve recovery. PURPOSE: Phase I/II trial to study the effectiveness of endoscopic placement of metal stents in treating patients who have cancer-related obstruction of the duodenum.

| 2004055 | ecrin-mdr-crc

Transcription profiling of mouse Rb1 deficient Apc1638N cecal tumors vs duodenal tumors

Project description:To examine the role of Rb1 in gastrointestinal (GI) tumors we generated mice with an Apc1638N allele, Rbtm2brn floxed alleles, and a villlin-cre transgene (RBVCA). These mice had reduced median survival due to an increase in tumor incidence and multiplicity in the cecum and the proximal colon; they differed from murine intestinal tumors of the Apc1638N type which normally arise solely in the small intestine. We have examined by micro-array analysis three cecal tumors from these mice (probable adenomas), and compared them to three duodenal tumors (probable adenocarcinomas). Expression profiles of duodenal and cecal tumors relative to each other show unique gene subsets up and down regulated. The two tumor types were subsequently shown to differentially regulate distinct sets of genes over expressed in a majority of human colorectal carcinomas. Experiment Overall Design: We have compared 3 cecal tumors with 3 duodenal tumors from Rb1 deficient Apc1638N mice.

2008-11-13 | E-GEOD-13298 | biostudies-arrayexpress

Genome-wide transcriptome profiling of human duodenal organoids, Duodenum Intestine-Chip and adult duodenal tissue using RNA-seq.

Project description:Genome-wide transcriptome profiling of human duodenal organoids, Duodenum Intestine-Chip and adult duodenal tissue using RNA-seq.

| PRJNA557703 | ENA

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