Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cytosine methylation profiling in two dimensional and extracellular matrix based three-dimensional cultures of breast cancer cells

ABSTRACT: Cytosine methylation profiling in two dimensional and extracellular matrix based three-dimensional cultures of breast cancer cells

PROVIDER: PRJNA540693 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells

Project description:Two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells

| PRJNA540691 | ENA

Cytosine methylation profiling in two dimensional and extracellular matrix based three-dimensional cultures of breast cancer cells

Project description:MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total DNA was extracted. Bisulfite treatment and BS-SEQ were carried out to profile global cytosine methylation in both culture conditions.

2019-05-02 | GSE130589 | GEO

Gene expression profiling in two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells

Project description:Gene expression profiling in two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells

| PRJNA540695 | ENA

Gene expression analysis of MCF7 breast cancer cells cultured as xenografts, in two dimensional cultures, in polyHEMA anchorage independent three dimansional cell culture models and in Matrigel three dimensional cultures.

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

MCF10A cells expressing HER2 and HER3 and grown in three-dimensional cultures

Project description:The tyrosine kinase receptors HER2 and HER3 play an important role in breast cancer. The HER2/HER3 heterodimer is a critical oncogenic unit associated with reduced relapse-free and decreased overall survival. We provide gene expression profile of the mammary epithelial cells MCF10A expressing HER2, HER3 or HER2/HER3 and grown in three-dimensional cultures for 15 days in the presence of heregulin, a known HER3-ligand that stabilizes and activates the HER2/HER3 heterodimer. The mammary epithelial cells MCF10A were transduced with retroviral vectors expressing HER2, HER3 or both. Cells from each group were grown for 15 days in three-dimensional cultures. At the end of the experiment, RNA was extracted for gene expression analysis.

2012-09-01 | E-GEOD-37009 | biostudies-arrayexpress

Two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-05-02 | GSE130591 | GEO

MCF10A cells expressing HER2 and HER3 and grown in three-dimensional cultures

2012-09-01 | GSE37009 | GEO

Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures

Project description:Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures

| PRJNA473515 | ENA

2013-10-30 | GSE47583 | GEO

Organotypic three-dimensional cancer cell cultures mirror drug responses in vivo: Lessons learned from the inhibition of EGFR signaling

Project description:Complex three-dimensional (3D) in vitro model systems that recapitulate human tumor biology are essential to better understand the pathophysiology of the disease and to aid in the discovery of novel anti-cancer therapies. 3D organotypic cultures exhibit intercellula communication, nutrient and oxygen gradients, and cell polarity that is lacking in traditional two-dimensional (2D) monolayer cultures. In the present study, we could demonstrate that 2D and 3D cancer models exhibit different drug sensitivities towards both targeted inhibitors of EGFR signaling and broad acting cytotoxic agents. Changes in the kinase activities of Erb family members and differential expression of apoptosis- and survival-associated genes before and after drug treatment may account for the differential drug sensitivities. Importantly, EGFR oncoprotein addiction was evident only in the 3D cultures mirroring the effect of EGFR inhibition in the clinic. Furthermore, targeted drug efficacy was strongly increased when incorporating cancer-associated fibroblasts into the 3D cultures. Taken together, we could provide conclusive evidence that complex 3D cultures are more predictive of the clinical outcome than their 2D counterparts. In the future, 3D cultures will be instrumental for understanding the mode of action of drugs, identifying genotype-drug response relationships and developing patient-specific and personalized cancer treatments.

2017-11-30 | GSE102722 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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