Rattus norvegicus
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ABSTRACT:
PROVIDER: PRJNA290724 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptional profiling of the Fischer Rat Thyroid (FRT) cells comparing polarizing cells grown as a confluent two-dimensional monolayer (2D culture system) with cells grown in matrigel where they acquire a three-dimensional follicular structure (3D culture system).The goal was to identify regulators of 3D epithelial thyroid polarization and follicle formation.
2016-11-24 | GSE71259 | GEO
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: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:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures.
2013-10-30 | GSE47583 | GEO
Project description:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures. Gene expression analysis of MCF7 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.
2013-10-30 | E-GEOD-47583 | biostudies-arrayexpress
Project description:Human bone marrow mesenchymal stromal cells (MSCs) are conventionally cultured as adherent monolayers on tissue culture plastic. MSCs can also be cultured as 3D cell aggregates (spheroids). Optimised 3D conditions (60,000 MSCs cultured as a spheroid for 5 days) inhibited MSC proliferation and induced cell shrinkage in the absence of cell death. Primary human MSCs isolated from 2 donors were cultured under both monolayer (2D MSCs) and optimised 3D (3D MSCs) conditions. High quality RNA was isolated from all samples, and global gene expression analysis was performed in duplicate (using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays) to identify gene expression changes in 3D compared to 2D MSC cultures.
2015-09-30 | E-MTAB-3795 | biostudies-arrayexpress
Project description:The objective of this study was to use RNAseq to determine which gene change in expression when LKR10 cells are grown in monolayers (2D) or methylcellulose on ultra low attachment plates (3D), which prevents attachment of cells to the plate and promotes formation of 3D sphere-like clusters. A secondary objective was to determine whether knockdown of Ankrd35 altered gene expression of specific genes in 2D or 3D.
2021-11-11 | GSE134063 | GEO
Project description:High-Grade Serous Ovarian Carcinoma (HGSOC) is the most common form of ovarian cancer and finding new treatments remains an unmet need. While drug discovery is typically performed in two-dimensional (2D) monolayers, three-dimensional (3D) culture systems better mimic in vivo conditions. However, a comprehensive comparison of 3D vs 2D ovarian cancer models is lacking. Here, we quantitatively compared the whole cell proteomic signatures of 4 ovarian cell lines—PEO1, PEO4, UWB1.289, and UWB1.289+BRCA1— with different status of BRCA genes grown, in 2D and in 3D. Using isobaric labeling proteomics, we quantified 6,404 proteins and identified 371 significantly and commonly altered proteins between 2D and 3D. Proteins upregulated in 3D were enriched for transmembrane transport and NADH:ubiquinone oxidoreductase Complex I, while energy metabolism and cell growth pathways also showed dimensionality-dependent changes. Notably, membrane-associated proteins were downregulated in spheroids, particularly EGFR in PEO1. Furthermore, 3D culture modulated the response to carboplatin, with increased expression of drug resistance-associated proteins, including NDUF family members in all spheroid models. These findings underscore how culture dimensionality influences both the molecular landscape and chemotherapeutic response of HGSOC cells and highlight candidate targets for overcoming carboplatin resistance.
2025-10-13 | PXD066652 | Pride
Project description:High-Grade Serous Ovarian Carcinoma (HGSOC) is is the most common form of ovarian cancer and finding new treatments remains an unmet need. While drug discovery is typically performed in two-dimensional (2D) monolayers, three-dimensional (3D) culture systems better mimic in vivo conditions. However, a comprehensive comparison of 3D vs 2D ovarian cancer models is lacking. Here, we quantitatively compared the whole cell proteomic signatures of 4 ovarian cell lines—PEO1, PEO4, UWB1.289, and UWB1.289+BRCA1— with different status of BRCA genes grown, in 2D and in 3D. Using isobaric labeling proteomics, we quantified 6,668 proteins and identified 412 significantly altered proteins between 2D and 3D. Proteins upregulated in 3D were enriched for transmembrane transport and oxidoreductase activity, while energy metabolism and cell growth pathways also showed dimensionality-dependent changes. Notably, membrane-associated proteins such as EGFR were downregulated in spheroids, particularly in PEO1 and PEO4. Furthermore, 3D culture modulated the response to carboplatin, with increased expression of drug resistance-associated proteins, including NDUF family members and ATP6V0A2, in all spheroid models. These findings underscore how culture dimensionality influences both the molecular landscape and chemotherapeutic response of HGSOC cells and highlight candidate targets for overcoming carboplatin resistance.
2025-10-13 | PXD062934 | Pride
Project description:In order to determine genes that are differentially expressed during angiogenesis, Human Umbilical Vein Endothelial Cells (HUVEC) were cultured as 3D cultures undergoing tubulogenesis in a 3D fibrin matrix, or cultured as monolayers on top of a 3D fibrin matrix. RNA was then collected, reverse transcribed to cDNA and hybridized to glass slide oligo arrays containing 19k human genes. Differentially expressed genes in HUVECs undergoing tubulogenesis were then determined by comparing 2D to 3D culture samples.
2009-10-29 | E-MEXP-2410 | biostudies-arrayexpress