Intestinal epithelial organoids

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human gut metagenome (24)
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Repository

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pride (24)
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Tissue

Epithelial cell (8)
Colon (5)
Small intestine (4)
Cell culture (4)
Small intestine epithelium (3)
Intestine (3)
Paneth cell of epithelium of small intestine (2)
Intestinal epithelium (2)
Intestinal epithelial cell maturation (1)
Gastric epithelium (1)
Multipotent stem cell (1)
Gastrointestinal tract (1)
Enterocyte (1)
Gut (1)
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Disease

Disease free (3)
Gastroesophageal adenocarcinoma (1)
Ischemia (1)
Bacterial infectious disease (1)
Colorectal cancer (1)
Crohn's disease (1)
Chronic kidney disease (1)
Colon cancer (1)

Technology Type

Mass Spectrometry (24)
Shotgun proteomics (11)
Bottom-up proteomics (5)
Data-independent acquisition (5)
SWATH MS (3)
Mass spectrometry assay (2)
Gel-based experiment (2)
Affinity purification coupled with mass spectrometry proteomics (2)
Illumina HiSeq 2500 (1)
Mass spectrometry (1)
HDMSE (1)
Top-down proteomics (1)
Data-dependent acquisition (1)

Instrument Platform

Illumina NovaSeq 6000 (31)
Illumina HiSeq 2500 (18)
NextSeq 500 (10)
Illumina HiSeq 4000 (9)
Illumina HiSeq 2000 (4)
Illumina NovaSeq X (2)
NextSeq 2000 (2)
Orbitrap Fusion Lumos (2)
10x Chromium with a target of 5,000 cells. Chromium Single Cell 3’ Library & Gel Bead Kit v2 (1)
10X Genomics reagent kit (1)
MACS (1)
10X Genomics Chromium (1)
NA (1)
N/A (1)
Q Exactive (1)
Orbitrap Eclipse (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - negative - reverse phase (1)
Liquid Chromatography MS - positive - hilic (1)

Publication Date

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2023 (42)
2020 (40)
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2021 (29)
2018 (19)
2019 (13)
2014 (12)
2015 (10)
2013 (8)
2017 (7)
2012 (5)
2011 (5)
2016 (4)
2010 (2)
2009 (2)

CHEBI ID

CHEBI:47013 (1)
CHEBI:57925 (1)
CHEBI:28013 (1)
CHEBI:15946 (1)
CHEBI:32796 (1)
CHEBI:15811 (1)
CHEBI:17710 (1)
CHEBI:30841 (1)
CHEBI:17625 (1)
CHEBI:48095 (1)
CHEBI:47977 (1)
CHEBI:4167 (1)
CHEBI:17138 (1)
CHEBI:17797 (1)
CHEBI:16349 (1)
CHEBI:44215 (1)
CHEBI:17552 (1)
CHEBI:16908 (1)
CHEBI:4170 (1)
CHEBI:29042 (1)
CHEBI:15729 (1)
CHEBI:44409 (1)
CHEBI:15422 (1)
CHEBI:15414 (1)
CHEBI:30794 (1)
CHEBI:30887 (1)
CHEBI:33198 (1)
CHEBI:30832 (1)
CHEBI:17482 (1)
CHEBI:1547 (1)

Metabolite Name

FAD (2)
3,4-Dimethyl-2-(1-pyrrolidinyl)-2-cyclopenten-1-one (1)
5-Ethyl-2-(1-pyrrolidinyl)-2-cyclopenten-1-one (1)
4-(3-hydroxybutyl)-2-methoxyphenol (1)
5-(4-methoxyphenyl)pent-1-en-3-one (1)
1-(4-hydroxyphenyl)-4-methylpent-1-en-3-one (1)
11-hydroxy-15-methoxy-6,8,20-trioxapentacyclo[10.8.0.0?,?.0?,?.0??,??]icosa-1(12),2(9),4,10,14,16,18-heptaen-13-one (1)
(±)-2-Butylthiazolidine (1)
6-{3,5-dihydroxy-4-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic acid (1)
({5-hydroxy-8-methyl-2-oxo-4-phenyl-2H,8H-pyrano[2,3-f]chromen-8-yl}methoxy)sulfonic acid (1)
(4-{5-hydroxy-8,8-dimethyl-2-oxo-2H,8H-pyrano[2,3-f]chromen-4-yl}phenyl)oxidanesulfonic acid (1)
Glyinflanin H (1)
(1S,2R,3S)-2,3-Dihydro-4-(4-hydroxyphenyl)-1H-phenalene-1,2,3-triol (1)
Moracin E (1)
Moracin D (1)
Kanzonol U (1)
3-methyl-4-(methylamino)-1,2-diphenylbutan-2-ol (1)
1-O-(2R-methoxy-hexadecyl)-sn-glycerol (1)
Pinostrobin 5-O-glucoside (1)
Agecorynin C (1)
5,6,7,8,3',4',5'-Heptamethoxyflavone (1)
Medicarpin 3-O-glucoside (1)
3,4,5-trihydroxy-6-{4-[3-(4-methoxyphenyl)-3-oxopropyl]phenoxy}oxane-2-carboxylic acid (1)
3,4,5-trihydroxy-6-{3-[3-(4-methoxyphenyl)-3-oxopropyl]phenoxy}oxane-2-carboxylic acid (1)
3,4,5-trihydroxy-6-[5-methoxy-2-(3-phenylpropanoyl)phenoxy]oxane-2-carboxylic acid (1)
3,4,5-trihydroxy-6-[3-(4-methoxyphenyl)-3-oxo-1-phenylpropoxy]oxane-2-carboxylic acid (1)
3,4,5-trihydroxy-6-{2-[3-(4-methoxyphenyl)-3-oxopropyl]phenoxy}oxane-2-carboxylic acid (1)
6-{4-[(E)-2-(3,5-dimethoxyphenyl)ethenyl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic acid (1)
3,4,5-trihydroxy-6-{3-methoxy-4-[(3-phenyloxiran-2-yl)methyl]phenoxy}oxane-2-carboxylic acid (1)
3,4,5-trihydroxy-6-{4-[3-(3-hydroxyphenyl)prop-2-en-1-yl]-3-methoxyphenoxy}oxane-2-carboxylic acid (1)

IsPrivate

False (1)

First Public Date

2025 (71)
2026 (63)
2024 (48)
2023 (48)
2022 (33)
2020 (28)
2021 (24)
2018 (17)
2019 (11)
2014 (9)
2017 (6)
2015 (4)
2016 (1)
2013 (1)

Classification

bacteria (3)

Modelling Approach

Ordinary differential equation model (1)

Study type

RNA-seq of coding RNA (42)
Transcription profiling by array (26)
RNA-seq of coding RNA from single cells (23)
Methylation profiling by array (6)
Cell line - High-throughput sequencing (4)
ChIP-seq (4)
High-throughput sequencing (2)
Comparative genomic hybridization by array (2)
DNA-seq (2)
Cell line - Single-cell sequencing (1)
RNA-seq of non coding RNA from single cells (1)
One-color microarray (1)
Human - Single-cell sequencing (1)
Human - One-color microarray (1)
ChIP-chip by array (1)
ScATAC-seq (1)
RNA-seq of total RNA (1)

Release Date

2022 (112)
2020 (92)
2025 (89)
2021 (89)
2024 (83)
2023 (82)
2018 (47)
2019 (36)
2015 (26)
2014 (20)
2017 (18)
2026 (16)
2016 (11)
2013 (10)
2012 (6)
2011 (5)
2010 (2)
2009 (2)

Lab affiliation

Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany Frankfurt Cancer Institute, Goethe University Frankfurt, 60596 Frankfurt/Main, Germany German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany (1)
Principal Investigator | The Ernst and Kaethe Ascher Career Development Chair | The Department of Immunology and Regenerative Biology | Weizmann-UK Building, Room 17 | Weizmann Institute of Science | Rehovot 76100, ISRAEL | Tel: +972-8-934-4937 (1)
Departmemnt of Pathology, University of Michigan (1)
University of Chicago Pritzker School of Medicine, Section of Nephrology, Chicago, IL 60637 USA (1)
Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany (1)
Head, Translational Antigen Discovery Lab Department of Medicine/ School of Clinical Sciences at Monash Health Monash University Level 7, TRF Building, Monash Medical Centre 246 Clayton Road Clayton VIC 3168 Australia M: +61 415126562 (1)
Department of Surgery, Maastricht University, Maastricht (1)
Chair in Infection and Global Health, Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, UK (1)
Washington University, St. Louis (1)
Novo Nordisk Foundation Center for Protein Research, UCPH, DK; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (1)
Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen - the Netherlands (1)
Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands (1)
Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool (1)
Université de Sherbrooke (1)
Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Brazil (1)
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany (1)
Institute of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, China. (1)
Newcastle University Biosciences Institute Cookson Building Newcastle University NE2 4HH United Kingdom (1)
Newcastle University Biosciences Institute Cookson Building Newcastle University NE2 4HH United Kingdom (1)
Department of Pharmacy, Uppsala University, Box 580, SE-751 23, Uppsala, Sweden (lab head) (1)
Department of Pharmaceutical Sciences, Utrecht University (1)
Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT (1)
Head of the Curie Institute Mass Spectrometry Platform (1)
Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA (1)

Tags

pathogen (3)
pathogen:bacterium (3)

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

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 characteri...

ORGANISM(S): Homo sapiens

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

Single intestinal stem cells build crypt-villus structures in vitro without a cellular niche

The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. We have recently demonstrated the presence of approximately six cycling Lgr5+ stem cells at the bottoms of small intestinal crypts1. We have now established long-term culture conditions under which single crypts und...

ORGANISM(S): Mus musculus

2009-04-03 | E-GEOD-14594 | biostudies-arrayexpress

RNA-seq of murine small intestinal organoids treated with type I PRMT inhibitor MS023 against untreated controls

Murine small intestinal organoids were cultured in the presence or absence of 5µM inhibitor MS023 (PubChem CID 92136227), which targets type I protein arginine methyltransferases Prmt1, Prmt3, Prmt4, Prmt6, Prmt8. Organoids were grown in culture media containing EGF, Noggin and R-spondin (ENR), medi...

ORGANISM(S): Mus musculus

2020-12-16 | E-MTAB-9291 | biostudies-arrayexpress

RNA-seq of small intestinal organoids treated with an inhibitor for the epigenetic modifier LSD1

To assess the role of LSD1 in mice small intestinal epithelium, small intestinal organoids were treated with an inhibitor for LSD1 (GSK-LSD1) and compared to untreated organoids. Similar to intestinal epithelium from mice with an intestinal epithelium specific LSD1-KO, paneth cells dissappear upon G...

ORGANISM(S): Mus musculus

2020-11-16 | E-MTAB-9077 | biostudies-arrayexpress

Epithelium-only cultured stem cells isolated from human pluripotent stem cell derived intestinal organoids grown in matrigel and alginate

Human intestinal organoids were grown in a typical 3D matrigel culture environment, or in an alginate gel, then a subset from each condition were xenotransplanted to vascularized and mature in vivo. Epithelium was isolated and epithelial only organoids (enteroids) were then grown from each condition...

ORGANISM(S): Homo sapiens

2019-06-27 | E-MTAB-7000 | biostudies-arrayexpress

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

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 ...

ORGANISM(S): Homo sapiens

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

RNA-seq of murine small intestinal organoids treated with Ep300/Crebbp inhibitor I-CBP112 against untreated controls

Murine small intestinal organoids were cultured in the presence or absence of 3µM inhibitor I-CBP112 (PubChem CID 90488984), which targets E1A Binding Protein P300 (Ep300) and Creb-binding protein (Crebbp, Cbp). Organoids were grown in culture media containing EGF, Noggin and R-spondin (ENR), media ...

ORGANISM(S): Mus musculus

2020-12-16 | E-MTAB-9290 | biostudies-arrayexpress

scRNA-seq of intestinal epithelial organoids derived from human fetal duodenum

Here, we used single-cell RNA-sequencing (scRNA-seq) to profile intestinal epithelial only organoids (also known as enteroids) from human fetal duodenum after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added.

ORGANISM(S): Homo sapiens

2022-07-17 | E-MTAB-11912 | biostudies-arrayexpress

Long-term in vitro expansion of epithelial organoids from human colon, adenoma, adenocarcinoma and Barrett's Esophagus

Background & Aims: We have recently established long-term culture conditions under which single crypts or stem cells derived from murine small intestine expand over long periods of time. Growing crypts undergo multiple crypt fission events, whilst simultaneously generating villus-like epithelial dom...

ORGANISM(S): Homo sapiens

2011-12-07 | E-GEOD-28907 | biostudies-arrayexpress

RNAseq of small intestinal organoids from mice treated with the cytokines IL-13 and IL-22 for 72 hours in combination with the BMP signaling inhibitor DMH1

The intestinal epithelium is our first line of defense against infections of the gut and the plasticity in cellular differentiation of the intestinal epithelium is an important part of this response. The changes in cellular composition is driven by immune cell derived cytokines. Here we use signatur...

ORGANISM(S): Mus musculus

2022-05-08 | E-MTAB-9185 | biostudies-arrayexpress

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