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DNA topology analysis reveals stable compartments and TADs in malignant and normal uveal melanocytes as novel molecular features of uveal melanoma

ABSTRACT: DNA topology analysis reveals stable compartments and TADs in malignant and normal uveal melanocytes as novel molecular features of uveal melanoma

PROVIDER: PRJNA832766 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18944283_1.fastq.gz	Fastqsanger.gz
	SRR18944283_2.fastq.gz	Fastqsanger.gz
	SRR18944284_1.fastq.gz	Fastqsanger.gz
	SRR18944284_2.fastq.gz	Fastqsanger.gz
	SRR18944285_1.fastq.gz	Fastqsanger.gz

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DNA topology analysis reveals stable compartments and TADs in malignant and normal uveal melanocytes as novel molecular features of uveal melanoma

Project description:To elucidate if regulation of gene expression could be linked to chromatin organization and DNA folding, we investigated the chromatin structure and DNA topology of two uveal melanoma models.

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Mass spectrometry-based profiling of histone posttranslational modifications in uveal melanoma tissue, human melanocytes, and uveal melanoma cell lines

Project description:Purpose: Epigenetic mechanisms and alterations in uveal melanoma (UM) development are still not well understood. In this pilot study, histone posttranslational modifications (PTMs), which are epigenetic mechanisms regulating gene expression, were analyzed in UM formalin-fixed paraffin-embedded (FFPE) tissues and control tissue as well as in UM cell lines and healthy melanocytes to provide a deeper insight into the pathogenesis of UM and the potentially prognostic relevance of these molecular markers. Methods: FFPE tissue of UM (n=24) and normal choroid (n=4) as well as human UM cell lines (n=7), human skin melanocytes (n=6) and uveal melanocytes (n=2), were analyzed by a quantitative mass spectrometry (MS) approach.

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Next generation sequencing analysis in uveal melanoma cells and normal melanocytes.

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2013-02-14 | E-GEOD-44296 | biostudies-arrayexpress

Histone acetylation modification analysis in uveal melanoma cells and normal melanocytes

Project description:In order to study the histone modification differences in uveal melanoma cells and normal melanocytes.

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Histone acetylation modification analysis in uveal melanoma cells and normal melanocytes.

Project description:In order to study the histone modification differences in uveal melanoma cells and normal melanocytes.

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Epigenome analysis of primary uveal melanoma cells, normal uveal melanocytes, neural crest stem cells, embryonic stem cells and uveal melanoma cell lines

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Epigenetics profiling of malignant uveal melanocytes reveals novel molecular features of uveal melanoma

Project description:Epigenetics profiling of malignant uveal melanocytes reveals novel molecular features of uveal melanoma

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PRAME induces genomic instability in uveal melanoma [RNA-seq]

Project description:RNA-seq of uveal melanoma cell lines and uveal melanocytes

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Differential responses of choroidal melanocytes and uveal melanoma cells to low oxygen conditions

Project description:PURPOSE: Tissue culture is traditionally performed at atmospheric oxygen concentration (21%), which induces hyperoxic stress, as endogenous physiologic oxygen tension found in tissues varies between 2% and 9%. This discrepancy may lead to misinterpretation of results and may explain why effects observed in vitro cannot always be reproduced in vivo and vice versa. Only a few studies have been conducted in low physiologic oxygen conditions to understand the development and differentiation of cells from the eye. METHODS: The aim of this study was to investigate the growth and gene expression profile of melanocytes from the choroid permanently exposed to 21% (hyperoxic) or 3% (physiologic) oxygen with proliferation assays and DNA microarray. The cellular behavior of the melanocytes was then compared to that of cancer cells. RESULTS: The gross morphology and melanin content of choroidal melanocytes changed slightly when they were exposed to 3% O2, and the doubling time was statistically significantly faster. There was an increase in the percentage of choroidal melanocytes in the active phases of the cell cycle as observed by using the proliferation marker Ki67. The caveolin-1 senescence marker was not increased in choroidal melanocytes or uveal melanoma cells grown in hyperoxia. In comparison, the morphology of the uveal melanoma cells was similar between the two oxygen levels, and the doubling time was slower at 3% O2. Surprisingly, gene expression profiling of the choroidal melanocytes did not reveal a large list of transcripts considerably dysregulated between the two oxygen concentrations; only the lactate transporter monocarboxylate transporter (MCT4) was statistically significantly upregulated at 3% O2. CONCLUSIONS: This study showed that the oxygen concentration must be tightly controlled in experimental settings, because it influences the subsequent cellular behavior of human choroidal melanocytes.

2016-09-10 | GSE86789 | GEO

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