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Homo sapiens

ABSTRACT: Genome wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells

PROVIDER: PRJNA277863 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1909122.fastq.gz	Fastqsanger.gz
	SRR1909123.fastq.gz	Fastqsanger.gz
	SRR1909124.fastq.gz	Fastqsanger.gz
	SRR1909125.fastq.gz	Fastqsanger.gz

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Genome wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells

Project description:TOP2B is involved in transcriptional initiation in response to nuclear hormone ligands and plays a role in transcriptional elongation. Whole genome TOP2B ChIP-seq was carried out on human MCF7 cells in the presence and absence of the nuclear hormone estradiol. Three peak calling methods were used and the peaks identified by at least two methods were analyzed further. Approximately half of the peaks fell either within a gene or within 5Kb of a transcription start site. The coincidence of TOP2B peaks and gene promoters was analyzed; TOP2B peaks were less frequently associated with promoters in estradiol treated than in control cells, suggesting a role of TOP2B in repression of transcription or a transient role in estradiol induced transcriptional changes. Whole genome TOP2B ChIP-seq was carried out on human MCF7 cells in the presence (30 mins exposure) and absence of the nuclear hormone estradiol. "Input" control samples were also sequenced for background detection and comparison.

2015-09-21 | E-GEOD-66753 | biostudies-arrayexpress

H3K27me3 ChIP-seq profiling in MCF7 cell lines under hypoxia

Project description:Purpose: Study hypoxia induced changes in genome-wide H3K27me3 occupancy Methods: Using the MCF7 breast epithelial adenocarcinoma cell line as a model, we studied epigenomic reprogramming as a function of fluctuating oxygen tension. To this end, we combined chromatin-immunoprecipitation and deep-sequencing analysis to identify H3K27me3-marks in MCF7 cells subjected to changes in oxygenation (i.e. acute hypoxia, chronic hypoxia). Results: H3K27me3-marks showed a rapid global increase at specific sites throughout the genome under hypoxia, both genic and inter-genic. Conclusions: Our data show that oxygen availability dynamically regulates the epigenetic state of the genome. Genome-wide H3K27me3-mark profiles were generated by combining ChIP analysis with deep sequencing using Illumina GAIIx.

2014-09-26 | E-GEOD-61740 | biostudies-arrayexpress

Genome wide ChIP-seq analysis of human TOP2B occupancy in KG-1 myeloid cell line

Project description:Genome wide ChIP-seq analysis of human TOP2B occupancy in KG-1 myeloid cell line

| PRJNA462843 | ENA

Genome wide ChIP-seq analysis of human TOP2B occupancy in KG-1 myeloid cell line

Project description:TOP2B is involved in transcriptional initiation in response to nuclear hormone ligands and plays a role in transcriptional elongation. Whole genome TOP2B ChIP-seq was carried out on human KG-1 cells in the presence and absence of the topoisomerase inhibitors mitoxantone and etoposide. Chromatin was assayed for TOP2B occupancy by peak calling with SISSRs and MACS.

2020-06-30 | GSE114048 | GEO

Transcription profiling of human breast cancer cell line MCF7 with FOXP3-induced gene expression

Project description:As we clarified before, the FOXP3 gene is an X-linked tumor suppressor gene in mammary carcinoma in both human and mouse. We also clarified that the ERBB2 and SKP2 oncogenes were transcriptionally under control of the FOXP3 gene product in mammary epithelial cells. In order to further clarify the FOXP3 down stream target genes in human breast cancer cells, we planed to conduct a microarray analysis of FOXP3-induced gene expression profiling. MCF7, a human breast cancer cell line, with FOXP3-tet-off system was cultured with and without Doxycyclin for 2 days. In the MCF7 cell cultured without Dox, the FOXP3 transcript was significantly induced as compared to the MCF7 cultured with Dox. Total RNA from MCF7 with and wihtout Dox were extracted by Qiagen's RNeasy column and they were applied to Affymetrix Human U133 2.0 array according to the manufacture's protocol. We clarified as yet unknown FOXP3 target genes in human epithelial cells, e.g., the p21 gene, by this analysis.

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ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters

Project description:We performed ChIP-seq in four cancer cell lines to identify ZFX binding sites throughout the human genome. We also performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucelosome, suggesting that ZFX may play a critical role in promoter architecture. We also showed that ZNF711 may function redundantly with ZFX in MCF7 by performing ZNF711 ChIP-seq and RNA-seq analysis after knockdown of ZFX, ZNF711, and both ZFX and ZNF711.

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Genome wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells

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H3K27me3 ChIP-seq profiling in MCF7 cell lines under hypoxia

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Effect of short-term glucose withdrawal on gene expression of MCF7 cells

Project description:MCF7 is an epithelial cell line isolated from the breast tissue of a patient with metastatic adenocarcinoma. Whether glucose autoregulates its own metabolism remains poorly understood. To probe this, we performed RNA-Seq analysis on MCF7 breast cancer cells cultured with/without short-term glucose withdrawal.

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