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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

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			Action	DRS
	SRR8997271_1.fastq.gz	Fastqsanger.gz
	SRR8997271_2.fastq.gz	Fastqsanger.gz
	SRR8997272_1.fastq.gz	Fastqsanger.gz
	SRR8997272_2.fastq.gz	Fastqsanger.gz
	SRR8997273_1.fastq.gz	Fastqsanger.gz

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

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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.

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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.

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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.

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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.

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

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

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