Ht29 - OmicsDI

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Unknown (1072)
Genomics (340)
Transcriptomics (311)
Proteomics (37)
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Organisms

Homo sapiens (337)
Andropogon gerardi (28)
Bacteria (28)
Canis lupus familiaris (28)
Clostridium perfringens (28)
Cnidaria (28)
Cricetulus griseus (28)
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synthetic construct (3)
human gut metagenome (2)
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Organisms

Homo sapiens (234)
Mus musculus (5)
human gut metagenome (2)
Vibrio vulnificus MO6-24/O (1)
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Lactiplantibacillus plantarum (1)

Repository

ENA (298)
biostudies-arrayexpress (180)
geo (165)
pride (28)
EGA (7)
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jPOST (3)
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NODE (1)

Tissue

Epithelial cell (13)
Cell culture (12)
Colon (6)
Blood cell (2)
HT-29 cell (2)
Blood platelet (1)
Colonic cancer cell line (1)
Colorectal adenocarcinoma cell line (1)
Fibroblast (1)
Hepatocyte (1)
Malignant cell (1)
Neuron (1)
Permanent cell line cell (1)
Rectum (1)
Stem cell (1)

Disease

Colon cancer (13)
Colorectal adenocarcinoma (3)
Colorectal cancer (3)
Colorectal carcinoma (2)
Disease free (2)
Non-small cell lung carcinoma (2)
Adenoma (1)
Maligant fibrousd histiocytoma post larynx carcinoma (1)
Colonic adenocarcinoma (1)
Colorectal Neoplasms (1)
Cardiovascular system disease (1)
Crohn's disease (1)
Lung adenocarcinoma (1)

Technology Type

Mass Spectrometry (28)
Shotgun proteomics (13)
Bottom-up proteomics (7)
Mass spectrometry (4)
Affinity purification coupled with mass spectrometry proteomics (4)
Data-dependent acquisition (3)
Mass spectrometry assay (1)
Affinity proteomics (1)
Data-independent acquisition (1)
Immunopeptidomics (1)
Top-down proteomics (1)

Instrument Platform

Illumina HiSeq 4000 (6)
Illumina NovaSeq 6000 (4)
Liquid Chromatography MS - positive - reverse phase (4)
Illumina MiSeq (3)
NextSeq 500 (3)
Q Exactive (3)
NA (2)
Illumina HiSeq 2000 (2)
Liquid Chromatography MS - negative - reverse phase (2)
PCR machine; AMPure XP beads; TruSeq Stranded mRNA stranded prep. kit (1)
PCR machine; Superscript II polymerase Kit (Invitrogen); PCR machine; AMPure XP beads; TruSeq stranded mRNA sample prep kit.; TruSeq Stranded mRNA stranded prep. kit (1)
Centrifuge 5424R (Eppendorf); miRNeasy Mini Kit (Qiagen); TURBO^TM DNase (Ambion); Bioanalyser (Agilent) (1)
Centrifuge 5424R (Eppendorf); RNAprotect Bacteria Reagent (Qiagen); Cell culture dish (Nunc) (1)
Centrifuge 5424R (Eppendorf); RNAprotect Bacteria Reagent (Qiagen) (1)
PCR machine; MICROBExpress kit (Ambion); TruSeq Stranded mRNA stranded prep. kit (1)
PCR machine; AMPure XP beads; TruSeq stranded mRNA sample prep. kit. (1)
Illumina Genome Analyzer IIx (1)
NextSeq 2000 (1)
Illumina iSeq 100 (1)
DNBSEQ-G400 (1)
HiSeq X Ten (1)
Illumina HiSeq 1500 (1)
NanoACQUITY UPLC (1)
Orbitrap Fusion (1)
Orbitrap Fusion Lumos (1)
Synapt G2-S HDMS (1)
MS Imaging - (1)
Bruker Ultraflex (1)

Publication Date

2013 (37)
2025 (33)
2026 (30)
2014 (29)
2023 (24)
2016 (23)
2009 (23)
2015 (22)
2021 (21)
2024 (19)
2022 (19)
2012 (18)
2011 (18)
2010 (17)
2020 (14)
2008 (14)
2017 (11)
2018 (7)
2019 (6)
2005 (4)
2007 (3)
2004 (1)
2006 (1)
2002 (1)

CHEBI ID

CHEBI:194285 (1)
CHEBI:149460 (1)
CHEBI:149457 (1)
CHEBI:149459 (1)
CHEBI:149450 (1)
CHEBI:149447 (1)
CHEBI:149456 (1)
CHEBI:149454 (1)
CHEBI:149452 (1)
CHEBI:149449 (1)
CHEBI:149442 (1)
CHEBI:66860 (1)
CHEBI:86243 (1)
CHEBI:34302 (1)
CHEBI:17256 (1)
CHEBI:169798 (1)
CHEBI:68434 (1)
CHEBI:10022 (1)
CHEBI:64517 (1)
CHEBI:27676 (1)
CHEBI:60943 (1)
CHEBI:28376 (1)
CHEBI:82969 (1)
CHEBI:16958 (1)
CHEBI:61204 (1)
CHEBI:53486 (1)
CHEBI:17509 (1)
CHEBI:15843 (1)
CHEBI:16235 (1)
CHEBI:33508 (1)

Metabolite Name

Sclerosporide (1)
4-amino-2,3-dihydroxy-N-[1-(8-hydroxy-1-oxo-3,4-dihydroisochromen-3-yl)-3-methylbutyl]hexanediamide (1)
Altoprev Lovastatin (1)
PhytoS1P (1)
Preaspernidgulene A2 (1)
Acyl carnitine C16:2 (1)
Botcinin A (1)
Ubiquinol 50 (1)
D-Geodin (1)
(2S)-2-[(2S,3S)-3-amino-5-oxooxolan-2-yl]-2-hydroxy-N-[(1S)-1-[(3S)-8-hydroxy-1-oxo-3,4-dihydroisochromen-3-yl]-3-methylbutyl]acetamide (1)
Emeriphenolicin E (1)
Preaspernidgulene A1 (1)
Dahliane J (1)
2-tetradec-7-enoyl-sn-glycerol 3-phosphate (1)
Cis-7-tetradecenoyl-D-asparagine (1)
Triprostatin B (1)
ACMC-20mleh (1)
12 hete (1)
(E)-9-(4-aminophenyl)-7-hydroxy-2,4,6-trimethyl-9-oxonon-2-enoic acid (1)
4-[2-(aminomethyl)-2-(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-(pentan-3-ylamino)benzoic acid (1)
N-[(3R,7R)-(?)-(9,10)-Dihydrojasmonoyl]-(S)-isoleucine (1)
Sperabillin C (1)
Ubiquinol-2 (1)
(6R)-3-(1H-indol-3-ylmethyl)-1-methyl-6-(2-methylpropyl)piperazine-2,5-dione (1)
Deoxy-AMP (1)
2'',3''-Cyclic AMP (1)
Cyclo(leu-trp) (1)
Lipoamide B (1)
Gamma-GLU-TYR (1)
[(1R,5R)-5-hydroxy-4-methoxy-1,5-dimethyl-2,6-dioxocyclohex-3-en-1-yl] 2-methylbutanoate (1)

First Public Date

2014 (50)
2024 (47)
2026 (34)
2025 (32)
2023 (27)
2021 (21)
2022 (20)
2020 (18)
2017 (14)
2015 (11)
2019 (10)
2018 (5)
2013 (5)
2016 (4)

Modelling Approach

Ordinary differential equation model (1)

Study status

Not provided (1)

Lab affiliation

Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands (2)
Laboratory of Systems Biology, Institute of Biomedical Chemistry, Moscow (2)
Center for Proteomics and Metabolomics Leiden University Medical Center (1)
Center of Neurodegenerative Diseases (1)
Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet SE 17177 Stockholm, Sweden. Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia. (1)
Clinical Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University) (1)
Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran (1)
Department of Biochemistry, Soonchunhyang University, College of Medicine, 31 Suncheonhyang 6-gil, Bongmyeong-dong, office# 310, Cheonan-si, Chungcheongnam-do, 31151, Republic of Korea (1)
Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea (1)
Division Head, WEHI (1)
EPFL (1)
Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC) (1)
Institute for Tumor Biology and Experimental Therapy Georg-Speyer-Haus 60596 Frankfurt/Main Germany (1)
Institute of Exptl. Internal Medicine Medical Faculty, University Magdeburg Leipzigerstr. 44 39120 Magdeburg, Germany (1)
Institute of Molecular Cancer Research, University of Zurich, Switzerland (1)
Lab's head (1)
MD, MSc, PhD Department of Clinical and Molecular Medicine asmund.flobak@ntnu.no +47 72573717 Gastrosenteret, Øya, Olav Kyrres gate 13 (1)
Malaker Lab Yale University Department of Chemistry (1)
OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands (1)
Prof. of Pharmacology Department of Neuroscience, Imaging and Clinical Sciences Director of Systems Pharmacology Lab, CeSI-MeT G. d’Annunzio” University, School of Medicine 66100 Chieti, Italy (1)
Protim, Inserm U1085 Irset (1)
Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK (1)
Team Lead in Proteomics Head of the Proteomics Research Translational Technology Platform, UCL Cancer Institute, Paul O’Gorman Building 72 Huntley Street, London, WC1E 6DD, UK (1)
The Proteomics Facility (1)
University of Oxford (1)
Walter and Elisa Hall Institute of Medical Research Inflammation Division (1)

Keyword

Intestinal microbiome (1)
Postoperative complications (1)
Mechanical bowel preparation (1)
Anastomotic leakage (1)

IsPrivate

False (1)

Classification

bacteria (1)

Modification

15.994915 (3)
227.126991 (1)
57.021464 (1)
9.030194 (1)

Study type

Transcription profiling by array (121)
RNA-seq of coding RNA (18)
Other (4)
ChIP-seq (4)
DNA-seq (4)
Unknown experiment type (3)
Transcription profiling by RT-PCR (3)
Comparative genomic hybridization by array (3)
ChIP-chip by tiling array (2)
RNAi profiling by array (2)
Exome sequencing (2)
MicroRNA profiling by array (2)
Methylation profiling by array (2)
Transcription profiling by SAGE (1)
Cell line - One-color microarray (1)
Cell line - High-throughput sequencing (1)
ChIP-chip by array (1)
4C (1)
CUT&RUN (1)
RNA-seq of coding RNA from single cells (1)
Methylation profiling by high throughput sequencing (1)
RNA-seq of non coding RNA (1)
Observational (1)

Release Date

2022 (136)
2023 (121)
2021 (101)
2020 (97)
2025 (79)
2016 (74)
2024 (73)
2018 (73)
2019 (70)
2015 (59)
2017 (59)
2014 (56)
2013 (48)
2011 (47)
2012 (42)
2010 (40)
2009 (23)
2008 (16)
2026 (12)
2005 (5)
2006 (4)
2007 (3)
2001 (3)
1999 (3)
2004 (2)
2003 (2)
2000 (2)
1998 (2)

Location

France (1)

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Single cell lipidomics of adherent gut epithelial cell lines Caco2 and HT29-MTX reveals a metabolic switch

Raw MS data files for the CaCo02 and HT29-MTX single cells isolated using the Yokogawa SS2000 for the research article 'Single cell lipidomics of adherent gut epithelial cell lines Caco2 and HT29-MTX reveals a metabolic switch'

2026-03-18 | MTBLS14074 | MetaboLights

Mass Spectrometry Imaging of Lipids in a Gut Epithelial Cell Model

Scope: The Caco2/HT29-MTX co-culture system is widely used as a cell model of the intestinal epithelium. Although the gut epithelium plays an important role in the uptake of free fatty acids and the resynthesis of triglycerides, the lipid distribution profile of the two-dimensional co-culture sys...

2025-06-14 | MTBLS12599 | MetaboLights

B-Raf inhibitors induce epithelial differentiation in BRAF mutant colorectal cancer cells

Mutations in the BRAF proto-oncogene, which encodes the B-Raf kinase, are associated with more aggressive, less-differentiated and therapy-resistant colorectal cancers (CRC). However, the molecular mechanisms responsible for these correlations remain unknown. Here, we report the characterization of ...

ORGANISM(S): Homo sapiens

2014-12-21 | E-GEOD-50791 | biostudies-arrayexpress

miRNA profiling of EV71 infected HT29 cells

HT29 cells was infected with EV71 at MOI 1 or nil respectively and harvested at 36hpi We use miRNA microarray to profile and identify miRNA which are up or down regulated due to EV71 infection 3 biological replicate (6 samples)

ORGANISM(S): Homo sapiens

2014-05-08 | E-GEOD-57372 | biostudies-arrayexpress

Transcription profiling of human HT29 cells sensitive and resistant to 10e-5M methotrexate

The abstract of the associated publication (Selga E, NoÃ© V, Ciudad CJ. Biochemical Pharmacology 2007 Sep 8; Article in press) is the following:; While studying differentially expressed genes between sensitive and 10-5 M Methotrexate (MTX) resistant HT29 human colon cancer cells, we identified some ...

ORGANISM(S): Homo sapiens

2008-06-16 | E-GEOD-9412 | biostudies-arrayexpress

RNA stearic HT29

Investigating the role of fatty acid on HT29 cells in the CRC context

ORGANISM(S): Homo sapiens

2025-01-01 | E-MTAB-14429 | biostudies-arrayexpress

siRNA profiling of human colon cancer HT29 cells, siHX transfected vs. control

HT29 cells were transsfected with siRNA (siHX), which is targeting the human endogeous retrovirus HERV-HX. Cells were harvested 72 h after transfection and knock-down of HERV-HX was evaluated by quantitative RT-PCR. Experiment Overall Design: Two-condition experiment, siHX vs. control cells. 1 trans...

ORGANISM(S): Homo sapiens

2009-01-14 | E-GEOD-14257 | biostudies-arrayexpress

Global and phosphoproteomics in control and TP53RK-deficient HT29 cells

We compared the global proteome and phosphoproteome between control and TP53RK-deficient HT29 cells using tandem mass tag (TMT) labeling for quantitative analysis.

ORGANISM(S): Homo sapiens (Human)

2025-10-27 | PXD061604 | Pride

RNA stearic HT29

PRJEB79772 | ENA

3C-seq of HT29 cells with CCAT1-L knockdown or scramble knockdown

CCAT1-L is a highly expressed long noncoding RNA located in the colorectal cancer specific super enhance region about 500 kb upstream of MYC gene. Knockdown of CCAT1-L significantly down-regulated interaction frequency between CCAT1 and MYC locus and repress MYC expression, suggesting a long-range c...

ORGANISM(S): Homo sapiens

2014-02-22 | E-GEOD-55261 | biostudies-arrayexpress

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