Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA273993 | ENA |
REPOSITORIES: ENA
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Project description:Colorectal cancers have a rare population of cells that express specific cell surface markers, and are referred to as cancer stem cells (CSC). Targeting CSCs, implicated in tumor relapse, is a paradigm shifting approach for colorectal cancer. We used gene microarray to analyze gene expression in HT-29, a colon cancer cell line, grown as monolayer and spheroid and identify metabolic pathways that are upregulated. HT-29 monolayer cells were grown in DMEM/F12 media supplemented with 10% FBS, and 1X Antibiotic-Antimycotic liquid (AA); and spheroids were grown in stem cell media [DMEM:F12, 1X AA, 1X B27, epidermal growth factors, and fibroblast growth factor for five days. Total RNA was isolated using the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol. RNA intergrity was confirmed on the Nanodrop ND-1000 and analyzed with Agilent 2100 bioanalyzer. The arrays were scanned with the Affymetrix 3000 7G plus scanner.
2015-04-01 | E-GEOD-65433 | biostudies-arrayexpress
Project description:Expression data of colorectal cancer HT-29 cells
| PRJNA390254 | ENA
Project description:Colorectal cancers have a rare population of cells that express specific cell surface markers, and are referred to as cancer stem cells (CSC). Targeting CSCs, implicated in tumor relapse, is a paradigm shifting approach for colorectal cancer. We used gene microarray to analyze gene expression in HT-29, a colon cancer cell line, grown as monolayer and spheroid and identify metabolic pathways that are upregulated.
2015-04-01 | GSE65433 | GEO
Project description:Microarray based mRNA profiling was used to charactarize and compare the gene expression in cells grown as monolayer or spheroids. Microarray based mRNA profiling was used to charactarize and compare the gene expression in cells grown as monolayer or spheroids.
2012-08-31 | E-GEOD-36666 | biostudies-arrayexpress
Project description:Microarray based mRNA profiling was used to charactarize and compare the gene expression in cells grown as monolayer or spheroids. Keywords: Expression profiling by array Microarray based mRNA profiling was used to charactarize and compare the gene expression in cells grown as monolayer or spheroids.
2014-02-17 | E-GEOD-53631 | biostudies-arrayexpress
Project description:To characterize cells cultured in 3D culture system using NanoCulture plates (NCPs) (Scivax) and in 2D culture, we examined gene expression in HT-29 cells on day 1 or day 7 on NCPs or 2D monolayer culture, using DNA microarrays. From our study, tumour cells grown on NCPs were morphologically different from cells in 2D monolayers, and the cells on NCPs actively migrated and aggregated to form multicellular spheroids (MCSs). To characterize this cell migration and intercellular adhesion, we compared gene expression in HT-29 cells on day 1 on NCPs and 2D monolayer culture using DNA microarrays. We could not find any significant difference in gene expression related to cell migration or cell-cell adhesion between cells grown on NCPs and as 2D monolayers on day 1, showing that cells on NCPs migrated and aggregated without any changes in gene expression (3D Day1 vs 2D Day1 2Fold change.xls). We next characterized mature 3D MCSs on NanoCulture plates, by comparing the gene expression profile of MCSs on day 7 and day 1 (3D Day7 vs 3D Day 1 2Fold change.xls). On day 7, we found a statistically significant increase in the expression of genes related to multicellular organization, intercellular signalling and the response to hypoxia. DNA microarray analysis also showed that the expression of genes that have been reported to be target genes for the transcription factor hypoxia-inducible factor 1 (HIF-1) (Ke, Q. & Costa, M. Hypoxia-inducible factor-1 (HIF-1). Mol Pharmacol 70, 1469-1480 (2006); Semenza, G.L. Defining the role of hypoxia-inducible factor 1 in cancer biology and therapeutics. Oncogene 29, 625-634.) was increased on day 7. When compared day 7 with 2D culture cells, the same tendency was observed (3D Day7 vs 2D Day 7 2Fold change.xls).
2010-08-25 | GSE23773 | GEO
Project description:HT-29 and HCT-116 cells were barcoded using the CloneTracker lentiviral barcode library and then dabrafenib and irinotecan resistant derivatives of these cell lines were established, respectively.10 million barcoded HT-29 and HCT-116 cells were seeded equally onto poly-HEMA coated 4xT75 flask (DMSO Control, Replica A, B, C for each drug). After seeding, cells were allowed to form spheroids and barcoded 3D-HT-29 spheroids were treated with dabrafenib at increasing doses starting from IC50/10 dose until IC50/2 dose with monthly doubling of the dosing (16 weeks), and barcoded 3D-HCT-116 cells were treated with irinotecan at increasing doses starting from IC50/4 dose until IC50 dose with weekly doubling of the dosing (4 weeks). Following the end points of treatment for each cell line, DNA was isolated from harvested cell lines and barcode sequencing and whole exome sequencing were carried out.
2023-09-01 | E-MTAB-13216 | biostudies-arrayexpress
Project description:To characterize cells cultured in 3D culture system using NanoCulture plates (NCPs) (Scivax) and in 2D culture, we examined gene expression in HT-29 cells on day 1 or day 7 on NCPs or 2D monolayer culture, using DNA microarrays. From our study, tumour cells grown on NCPs were morphologically different from cells in 2D monolayers, and the cells on NCPs actively migrated and aggregated to form multicellular spheroids (MCSs). To characterize this cell migration and intercellular adhesion, we compared gene expression in HT-29 cells on day 1 on NCPs and 2D monolayer culture using DNA microarrays. We could not find any significant difference in gene expression related to cell migration or cell-cell adhesion between cells grown on NCPs and as 2D monolayers on day 1, showing that cells on NCPs migrated and aggregated without any changes in gene expression (3D Day1 vs 2D Day1 2Fold change.xls). We next characterized mature 3D MCSs on NanoCulture plates, by comparing the gene expression profile of MCSs on day 7 and day 1 (3D Day7 vs 3D Day 1 2Fold change.xls). On day 7, we found a statistically significant increase in the expression of genes related to multicellular organization, intercellular signalling and the response to hypoxia. DNA microarray analysis also showed that the expression of genes that have been reported to be target genes for the transcription factor hypoxia-inducible factor 1 (HIF-1) (Ke, Q. & Costa, M. Hypoxia-inducible factor-1 (HIF-1). Mol Pharmacol 70, 1469-1480 (2006); Semenza, G.L. Defining the role of hypoxia-inducible factor 1 in cancer biology and therapeutics. Oncogene 29, 625-634.) was increased on day 7. When compared day 7 with 2D culture cells, the same tendency was observed (3D Day7 vs 2D Day 7 2Fold change.xls). HT-29 cells were maintained routinely as 2D monolayers in a humidified atmosphere of 5% CO2 in air at 37 °C in the growth medium recommended by suppliers. Exponentially growing cells were used in experiments, after trypsinization to detach them from the plates. Viable cells were counted using trypan blue dye-exclusion. For experiments, cells were seeded in 96-well plates at 1×10^4 cells/100 ul of NanoCulture Medium-M (Scivax) in either NCPs (Scivax), or in polystyrene plates for 2D monolayers, for 1 day or 7 days. Cells were collected and used for RNA extraction and DNA microarray analysis.
2010-08-25 | E-GEOD-23773 | biostudies-arrayexpress
Project description:Microarray based mRNA profiling was used to charactarize and compare the gene expression in cells grown as monolayer or spheroids.
2012-08-31 | GSE36666 | GEO
Project description:Expression data from HT-29, a human colonic epithelial cell line
| PRJNA193228 | ENA