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Homo sapiens

ABSTRACT: Genome-wide maps of chromatin accessibility of histone deacetylase inhibition in triple-negative breast cancer

PROVIDER: PRJNA358732 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5130180_1.fastq.gz	Fastqsanger.gz
	SRR5130180_2.fastq.gz	Fastqsanger.gz
	SRR5130181_1.fastq.gz	Fastqsanger.gz
	SRR5130181_2.fastq.gz	Fastqsanger.gz
	SRR5130182_1.fastq.gz	Fastqsanger.gz

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Homo sapiens

Project description:Genome-wide DNA methylation maps of histone deacetylase inhibition in triple-negative breast cancer

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Genome-wide maps of chromatin accessibility of histone deacetylase inhibition in triple-negative breast cancer

Project description:Analysis of chromatin accessibility changes after prolonged exposure of triple-negative breast cancer cell lines to low doses of Panobinostat (LBH589), a pan-histone deacetylase inhibitor.

2017-02-14 | GSE92898 | GEO

Histone deacetylase inhibition in triple-negative breast cancer

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Project description:Gene expression profiling of histone deacetylase inhibition in triple-negative breast cancer

| PRJNA358776 | ENA

Genome-wide DNA methylation maps of histone deacetylase inhibition in triple-negative breast cancer

Project description:Analysis of DNA methylation changes after prolonged exposure of triple-negative breast cancer cell lines to low doses of Panobinostat (LBH589), a pan-histone deacetylase inhibitor.

2017-02-14 | GSE92909 | GEO

Gene expression profiling of histone deacetylase inhibition in triple-negative breast cancer

Project description:Analysis of changes in gene expression levels after after prolonged exposure of triple-negative breast cancer cell lines to low doses of Panobinostat (LBH589), a pan-histone deacetylase inhibitor.

2017-02-14 | GSE92910 | GEO

Discrete Adaptive Responses to MEK Inhibitor In Subpopulations of Triple-Negative Breast Cancer [FAIRE-seq]

Project description:We report the chromatin accessibility of epithelial and mesenchymal subpopulations isolated from a triple-negative breast cancer cell line.

2021-11-10 | GSE138796 | GEO

Visualization and Sequencing of Accessible Chromatin Reveals Cell Cycle and Post-HDAC inhibitor Treatment Dynamics

Project description:Chromatin accessibility in the nucleus is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with lower mitochondrial DNA and duplicated sequences compared to ATACsee. Using NicE-viewSeq we interrogated cell cycle G1, S and G2M specific accessible chromatin in mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosome, chromatin accessibility remained subtly altered and generally preserved. Genome-wide alteration of accessibility for TSS and enhancer gradually decreased as the cell progressed from G1 to G2M, with distinctive differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylase promoted accessible chromatin of the gene body, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for MYC oncogene pathway correlated with gene down regulation. Surprisingly, repetitive RNA expression remained unaltered following histone acetylation mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility is a prerequisite during cell cycle and histone deacetylase inhibitor mediated therapeutics.

2020-09-09 | GSE139253 | GEO

Integration of ATAC-seq and RNA-seq identifies typing and prognosis evaluation target molecules of triple negative breast cancer

Project description:Molecular subtyping plays a vital role in the treatment of breast cancer, however, current clinical outcomes remain unsatisfactory despite having multiple molecular subtypes available, particularly for triple-negative breast cancers. Henceforth, our research primarily focuses on traditional molecular subtyping by utilizing transcriptome sequencing and ATAC-seq sequencing techniques to classify both tumor tissues and adjacent tissues from patients with breasts cancers into distinct groups. Through this process, we aim to identify key gene expressions involved in the development of breasts cancers as well as epigenetic characteristics influenced by alterations in chromatin accessibility patterns. Subsequently, employing conventional methods used for classifying breasts cancers into different molecular types enables us to further investigate significant variations observed specifically within triple-negative breasts cancers regarding their gene expression profiles and chromatin accessibility patterns. Lastly, utilizing data from TCGA database pertaining exclusively to cases involving triple-negative breasts cancers allows us to conduct regression analyses concerning our aforementioned findings while simultaneously selecting relevant molecular models closely associated with this particular subtype of breasts malignancy. Additionally evaluating how these differentially expressed genes influence prognosis through prognostic modeling analysis tailored towards predicting outcomes solely within cases involving individuals diagnosed with triple negative-breast malignancies will enable us ultimately construct an innovative model incorporating both gene expressions along with chromatin accessibility patterns as distinguishing features providing more substantial guidance towards improving clinical treatments targeting individuals afflicted by such conditions.

2025-01-01 | GSE254212 | GEO

Quantitative Phosphoproteome Analysis of Rocaglamide A in Triple-negative Breast Cancer cells

Project description:An TMT-based quantitative phosphoproteome analysis using liquid chromatography–coupled tandem mass spectrometry was performed to acquire proteome-wide expression data on Triple-negative Breast Cancer (TNBC) cells treated with time-course Rocaglamide A.

2025-01-04 | PXD048247 | JPOST Repository

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