Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analysis of HCT‑116 cells during in vitro culture over time

ABSTRACT: Human cancer cell lines are frequently used in controlled culture systems to investigate cancer biology. However, extended cultivation can introduce genomic and transcriptional instability. The cell line HCT-116 is a well characterized and widely used model for colorectal cancer. To assess transcriptome stability over time and characterize passage‑dependent gene expression changes, HCT‑116 cells were cultured for 25 consecutive passages (~16 weeks). Cells were harvested at passages 1, 5, 10, 15, 20, and 25, and total RNA was extracted for genome‑wide expression analysis. Microarray‑based transcriptome profiling was performed using the SurePrint G3 Human Gene Expression 8x60K v3 platform (Agilent, G4851C), and arrays were scanned with the InnoScan 910 system (Innopsys). Three biological replicates were included for each selected passage. Differential expression analysis was conducted to compare transcriptomic changes across passages and to identify potential shifts associated with prolonged in vitro cultivation.

ORGANISM(S): Homo sapiens

SUBMITTER: RGCC Central Europe GmbH

PROVIDER: E-MTAB-16637 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNAi knock down of mSin3a-b and SBTB4 in human colon carcinoma cell line HCT116

Project description:Efffects of silencing ZBTB4, mSin3a/mSin3b on HCT 116 human colon carcinoma cell lines for 48 hours

2008-03-31 | E-MEXP-1509 | biostudies-arrayexpress

Ginger compound [6]-shogaol activates Nrf2 in human colon epithelial cells

Project description:To identify the direct molecular targets of 6S, gene microarrays were used to profile gene expression in HCT-116 cells treated with 6S (20 uM for 24 h) comparing with HCT-116 cells treated with DMSO (control). Two-class comparisons. HCT-116 cells treated with 6S (20 uM for 24 h) vs. HCT-116 cells treated with DMSO control;Biological replicates: 4 replicates for each group.

2014-04-23 | E-GEOD-57006 | biostudies-arrayexpress

TRAP1 silencing in HCT116 cells

Project description:Trascription profiling analysis was performed on HCT-116 cell lines transiently silenced with TRAP1 compared with scrumble

2014-11-15 | E-MTAB-2500 | biostudies-arrayexpress

Optimized siRNAs with a minimal off-target effect facilitate the screening of essential genes in cancer cells

Project description:siRNAs with dN are a promising and easy approach to characterize essential genes by minimizing the off-target effect in cancer cells. mRNA profiles of HCT 116 cells after the transfection of siRNAs or blank control by deep sequencing, using HiSeq 2000

2015-07-01 | E-GEOD-62968 | biostudies-arrayexpress

Expression data from Che-1 (AATF) depleted HCT 116 cell line

Project description:Che-1 is a RNA Polymerase II binding protein involved in the regulation of gene transcription. Che-1 emerges as an important adaptor that connects transcriptional regulation, cell-cycle progression, checkpoint control, and apoptosis. We have observed that Che-1 depletion sensitizes cells to chemotherapy. We used microarrays analysis to investigate classes of genes regulated by Che-1. Total RNA was extracted from control and Che-1 depleted HCT 116 cells 48 hours after transient transfection of siRNA.

2013-03-12 | E-GEOD-45009 | biostudies-arrayexpress

RNA-seq of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine

Project description:We performed poly(A)+ stranded RNA-seq of a panel of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine. In parallel, we determined the genomic location and DNA methylation levels of human full-length LINE-1 elements (L1) from the same samples using bs-ATLAS-seq (E-MTAB-12240). To link DNA methylation and L1 expression, we used cell pellets from the same cell culture to perform both RNA-seq and bs-ATLAS-seq.

2023-09-21 | E-MTAB-12245 | biostudies-arrayexpress

SOX4 supports cancer stemness by enhancing HDAC1 transcription revealed by comparative proteomics

Project description:We have investigated the proteome changes induced by SOX4 overexpression in HCT-116 cells using iTRAQ-based quantitative proteomics. Bioinformatics analysis revealed that HDAC1 could be one of the important regulators in cancer stem cells (CSCs) maintenance. We found that SOX4 transcriptionally regulates HDAC1 to support the stemness of cancer stem cells (CSCs). This work revealed a novel underlying mechanism, SOX4-HDAC1 axis, for stemness maintenance of human cancer.

2021-09-09 | PXD019694 | Pride

Competitive activity-based protein profiling of LF-268 target engagement in live HCT-116 cells using a click handle-derivatized RAF inhibitor probe

Project description:Activity-based protein profiling using 268-TCO, a trans-cyclooctene (TCO)-derivatized analogue of the pan-RAF DFG-out inhibitor LF-268, to characterize intracellular target engagement in live HCT-116 (mutant KRAS/WT RAF) cells. Cells were pre-treated with LF-268 (5 µM) or DMSO as competitor, followed by treatment with 268-TCO probe. After lysis, probe-bound protein complexes were captured via click chemistry using tetrazine (Tz)-coupled sepharose beads. Enriched proteins were identified and quantified by label-free LC-MS/MS.

2026-04-20 | PXD075291 | Pride

Phosphoproteomic profiling of kinobead-enriched fractions from LF-268-treated HCT-116 cells via SILAC-based quantification

Project description:SILAC-based phosphoproteomic profiling of kinase-enriched fractions from HCT-116 cells treated with the DFG-out pan-RAF inhibitor LF-268 to characterize kinase signaling responses. Cells were metabolically labeled and treated with 1 µM LF-268 or DMSO for 1 hour, followed by serial kinobead enrichment and Fe³⁺-NTA IMAC phosphopeptide enrichment prior to LC-MS/MS.

2026-04-20 | PXD075307 | Pride

Proteomic approach for searching of universal, tissue-specific and line-specific markers of extracellular vesicles in lung and colorectal adenocarcinoma cell lines:extracellular vesicles only

Project description:The efficiency of anticancer therapy depends heavily on the molecular features of the tumor. Since tumor-derived extracellular vesicles, including exosomes, contain proteins that are characteristic for producer cells and could be detected in biological fluids, they are of great interest for screening of predictive biomarkers. We have performed label-free mass spectrometric profiling of extracellular vesicles originated from human colon cancer cell lines Caco-2, HT-26 and HCT-116, and from lung cancer cell lines NCI-H23 and A549.

2021-09-09 | PXD020467 | Pride

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