intestinal organoids

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Organisms

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unidentified (1)

Repository

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geo (552)
biostudies-arrayexpress (172)
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pride (37)
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Tissue

Epithelial cell (8)
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Enterocyte (2)
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Disease

Disease free (4)
Intestinal disease (2)
Malignant neoplasm of stomach (1)
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Cancer (1)
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Crohn's disease (1)
Gastroesophageal adenocarcinoma (1)
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Technology Type

Mass Spectrometry (40)
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Data-independent acquisition (6)
Mass spectrometry (4)
Mass spectrometry assay (4)
Data-dependent acquisition (4)
ESI (3)
SWATH MS (3)
Affinity purification coupled with mass spectrometry proteomics (2)
Gel-based experiment (2)
ILLUMINA, HiSeq X Ten (1)
Illumina HiSeq 2500 (1)
DiaPASEF (1)
HDMSE (1)
Top-down proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (42)
Illumina HiSeq 2500 (23)
Illumina HiSeq 4000 (16)
NextSeq 500 (16)
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Liquid Chromatography MS - negative - reverse phase (5)
Q Exactive (3)
Liquid Chromatography MS - positive - reverse phase (3)
NextSeq 2000 (2)
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10x Chromium with a target of 5,000 cells. Chromium Single Cell 3’ Library & Gel Bead Kit v2 (1)
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MACS (1)
10X Genomics Chromium (1)
BD FACSARIA III (1)
Fluidigm C1 (1)
NA (1)
N/A (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - positive - reverse-phase (1)
Liquid Chromatography MS - negative - reverse-phase (1)
Liquid Chromatography MS - positive - hilic (1)

Publication Date

2025 (112)
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2020 (86)
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2018 (38)
2019 (32)
2014 (30)
2017 (21)
2016 (18)
2015 (18)
2013 (10)
2012 (6)
2011 (6)
2010 (2)
2009 (2)

CHEBI ID

CHEBI:29042 (2)
CHEBI:48928 (2)
CHEBI:17561 (2)
CHEBI:4170 (2)
CHEBI:16865 (2)
CHEBI:17203 (2)
CHEBI:15729 (2)
CHEBI:17196 (2)
CHEBI:16977 (2)
CHEBI:17202 (2)
CHEBI:15428 (2)
CHEBI:16467 (2)
CHEBI:17053 (2)
CHEBI:17858 (2)
CHEBI:15891 (2)
CHEBI:17659 (2)
CHEBI:16349 (2)
CHEBI:17482 (2)
CHEBI:18019 (2)
CHEBI:16680 (2)
CHEBI:17552 (2)
CHEBI:15422 (2)
CHEBI:18012 (2)
CHEBI:32816 (2)
CHEBI:30887 (2)
CHEBI:16761 (2)
CHEBI:17345 (2)
CHEBI:32805 (2)
CHEBI:30915 (2)
CHEBI:16027 (2)

Metabolite Name

N8-Acetylspermidine (3)
Adipamide (3)
N6,N6,N6-Trimethyl-L-lysine (3)
Betaine (3)
Methyl dihydrojasmonate (3)
Palmitoylethanolamide (3)
Citrulline (3)
L-Lysine (3)
7-Methylguanine (3)
Kynurenic acid (3)
L-cysteine (3)
L-Asparagine (3)
Serotonin (3)
13-OxoODE (3)
N-Acetylornithine (3)
Biliverdin (3)
Indole (3)
N-Acetylneuraminic acid (3)
Taurine (3)
L-arginine (3)
2-Hydroxycaproic acid (3)
Oleamide (3)
L-Histidine (3)
Riboflavin (3)
Creatinine (3)
Creatine (3)
Stearamide (3)
L-Carnitine (3)
Bilirubin (3)
L-Phenylalanine (3)

First Public Date

2025 (136)
2026 (127)
2024 (109)
2023 (91)
2021 (79)
2020 (76)
2022 (72)
2018 (38)
2019 (33)
2017 (23)
2014 (21)
2015 (10)
2016 (9)
2013 (1)

Modelling Approach

Constraint-based model (1)
Ordinary differential equation model (1)

Study status

Recruiting (3)
Not yet recruiting (1)

Lab affiliation

Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea (2)
Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands (1)
Chair in Infection and Global Health, Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, UK (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)
Departmemnt of Pathology, University of Michigan (1)
Department of Anatomy and Cell Biology, Faculty of medecine and Health Sciences, Université de Sherbrooke (1)
Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool (1)
Department of Pharmaceutical Sciences, Utrecht University (1)
Department of Pharmacy, Uppsala University, Box 580, SE-751 23, Uppsala, Sweden (lab head) (1)
Department of Surgery, Maastricht University, Maastricht (1)
Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands (1)
Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada. (1)
Head of the Crick Mass Spectrometry Proteomics Platform (1)
Head of the Curie Institute Mass Spectrometry Platform (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)
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)
Institute of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, China. (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)
Max Planck Institute for Biology of Ageing, Cologne, Germany. Institute of Healthy Ageing, and Department of Genetics, Evolution and Environment, UCL, London, UK. (1)
Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT (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)
Novo Nordisk Foundation Center for Protein Research, UCPH, DK; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 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)
Professor of Molecular Biology. Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee ,Dundee, DD1 5EH, Scotland, UK (1)
Proteomics Center, Erasmus University Medical Center (1)
Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands. (1)
Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen - the Netherlands (1)

Keyword

Organoid (1)

IsPrivate

False (2)

Classification

bacteria (4)

Study type

RNA-seq of coding RNA (67)
Transcription profiling by array (37)
RNA-seq of coding RNA from single cells (28)
Methylation profiling by array (6)
Cell line - High-throughput sequencing (4)
ChIP-seq (4)
Observational (4)
High-throughput sequencing (3)
DNA-seq (3)
RNA-seq of total RNA (3)
Human - Single-cell sequencing (2)
Human - High-throughput sequencing (2)
Comparative genomic hybridization by array (2)
Cell line - Single-cell sequencing (1)
Baseline (1)
RNA-seq of non coding RNA from single cells (1)
Differential (1)
One-color microarray (1)
Human - One-color microarray (1)
Animal - High-throughput sequencing (1)
ChIP-chip by array (1)
Ribo-seq (1)
ScATAC-seq (1)
Single nucleus RNA sequencing (1)

Release Date

2022 (201)
2021 (157)
2023 (156)
2020 (156)
2025 (154)
2024 (152)
2018 (88)
2019 (70)
2017 (45)
2015 (39)
2014 (37)
2026 (31)
2016 (26)
2013 (13)
2012 (8)
2011 (7)
2010 (2)
2009 (2)

Location

Germany (3)

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Isotope Tracing Analysis in Intestinal Organoids with fructose

Not available

ORGANISM(S): Mus musculus

ST001622 | MetabolomicsWorkbench

Untargeted metabolomics of intestinal organoids treated with fructose

Not available

ORGANISM(S): Mus musculus

ST001621 | MetabolomicsWorkbench

Lipid Profiling of Mouse Intestinal Organoids for studying APC Mutations

Not available

ORGANISM(S): Mus musculus

ST001707 | MetabolomicsWorkbench

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 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

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

Human small intestinal organoids grown with a specific protocol to enrich for Paneth cells were treated with an inhbitor (GSK-LSD1) for the epigenetic modulator LSD1.

To assess the role of LSD1 in human intestinal epithelium, human small intestinal organoids were treated with an inhibitor for LSD1 (GSK-LSD1) and compared to untreated organoids. The organoids were grown with specific conditions where Paneth cells are present in the organoids as similar experiments...

ORGANISM(S): Homo sapiens

2020-11-16 | E-MTAB-7863 | 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

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

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

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