Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects

ABSTRACT: Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects

PROVIDER: PRJNA948350 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23955800_1.fastq.gz	Fastqsanger.gz
	SRR23955800_2.fastq.gz	Fastqsanger.gz
	SRR23955801_1.fastq.gz	Fastqsanger.gz
	SRR23955801_2.fastq.gz	Fastqsanger.gz
	SRR23955802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 230

Similar Datasets

Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects

Project description:The study was design to compare transcriptomic profiles of whole biopsies to enteroid/colonoid lines derived from them. In the accompanying publication, we observed substantial overlap of pathways upregulated in Crohn’s disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.

2023-08-22 | GSE228122 | GEO

Transcriptional response of human enteroids/colonoids on transwells to infection

Project description:The goal of this study was to evaluate the transcriptional response of human enteroids/colonoids on transwells to infections (bacterial and rotavirus). Enteroids/colonoids lines C103, C109, D103, D109, I103, I109, J2 and J11 were plated on transwells coated with Matrigel, differentiated, and inoculated (rotavirus (Ito), bacteria or mock) for 6 or 24 hours. Subsequently, total RNA was isolated and paired-end sequencing was performed.

2021-10-01 | GSE183222 | GEO

RNA-Sequencing of epithelium and colonoids from patients with pediatric inflammatory bowel disease

Project description:Objective: Children with very early onset inflammatory bowel disease (VEO IBD) present with more extensive, severe, and refractory disease than older children and adults with IBD. In the current study, we evaluated functional and transcriptomic differences in epithelial cells from patients with VEO and older onset IBD compared to controls. Design: We established enteroids and colonoid lines from patients with VEO and older onset IBD and control patients. We evaluated crypt conversion (initial growth efficiency) compared to histopathological and clinical parameters. We performed RNA-sequencing on colonoids followed by validation via qPCR and flow cytometry in additional patients and in colonoids after multiple passages. Results: Control enteroids and colonoids exhibited consistently high crypt conversion, whereas patients with VEO and older onset IBD exhibited decreased crypt conversion associated with higher inflammation scores. Transcriptomic analysis revealed increased expression of LYZ, reported previously in colonoids from adult patients with ulcerative colitis, as well as antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging as verified by flow cytometry. Conclusion: We present the first functional comparison of enteroids and colonoids from patients with VEO and older onset IBD, a subset of which exhibit poor initial growth. Enhanced and persistent expression of epithelial antigen presentation genes in patient colonoids supports the notion that epithelial cell-intrinsic differences may result from or contribute to disease. Analyses of colonoids from pediatric patients with IBD will contribute to a greater understanding of epithelial cell-autonomous defects in patients with VEO and older onset IBD and will be an important tool for understanding novel disease variants in the future.

2021-01-27 | GSE135170 | GEO

Calf ileum and rectum microbiota

Project description:Calf ileum and rectum microbiota Raw sequence reads

| PRJNA625122 | ENA

Novel lentiviral constructs for the specification of rare and ectopic cell types in human colonoids

Project description:In the past 15 years, organoid models have revolutionized the study of the human gastrointestinal (GI) epithelium. Organoids can be derived from patient tissue and grown as strictly epithelial structures referred to as enteroids and colonoids. Despite their utility, rare cell types are often absent in enteroids and colonoids. We hypothesized that induced expression of key transcription factors (TFs) would be sufficient to specify a subset of these cell types. To test this hypothesis, we generated lentiviral constructs that allow the inducible expression of cell-type specifying TFs. We transduced human enteroids and colonoids with these constructs and examined their ability to induce differentiated cell types.

2025-11-25 | GSE282845 | GEO

Transcriptional response of human enteroids/colonoids on transwells to infection

Project description:Transcriptional response of human enteroids/colonoids on transwells to infection

| PRJNA759635 | ENA

Transcription profiling of mouse conventional and germ-free ileum, colon and rectum

Project description:Whole tissues corresponding to the ileum, colon and rectum were dissected from adult mice and used for RNA preparation. The aim of experiment was to study the impact of gut microbiota on gene expression in different gut regions. Experiment Overall Design: Three biological replicates were used for each condition. Each RNA preparation was independently hybridized to one chip.

2008-06-20 | E-GEOD-3304 | biostudies-arrayexpress

Escherichia coli strain:rectum | isolate:rectum

Project description:Escherichia coli strain:rectum | isolate:rectum Genome sequencing

| PRJNA1031530 | ENA

Ileum Transcriptomic Profiling in Inflammatory Bowel Disease

Project description:We report ileum gene expression of 37 controls and 158 patients with either Crohn's disease (n=112), ulcerative colitis (n=44), unclassifed IBD (1), or IBS (1). We contrast gene expression in African American (n=104) versus white (n=25) CD and UC patients.

2020-04-15 | GSE137344 | GEO

RNA-seq of human epithelium-only colonic and small intestinal organoids derived from intestinal resections, biopsy specimens and cryopreserved crypts

Project description:Patient-derived gastrointestinal epithelium-only organoids from the small and large intestine, also referred to as colonoids and enteroids, were generated as part of the development of an on-going organoid biobank at the Michigan Medicine Translational Tissue Modeling Laboratory (TTML) (www.UmichTTML.org). Gene expression in organoids was characterized using RNA-sequencing

2020-07-24 | E-MTAB-9339 | 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