Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide mapping of histone methylation in human melanocytes and melanoma cell lines

ABSTRACT: Aberrant DNA methylation and histone modifications both contribute to carcinogenesis, but how these two epigenetic factors interact to impact gene expression remain unclear. To address this issue, we studied gene expression profiles, DNA methylation and two key histone modifications (H3K4me3 and H3K27me3), in two types of normal melanocytes (HEMn and HEMa) and two melanoma cell lines SK-MEL-28 and LOXIMVI. Using these data, we analyzed the relationship between epigenetic factors and gene expression status in both normal and melanoma cells, and the impact of epigenetic switches on gene expression during melanomagenesis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE33930 | GEO | 2013/12/01

SECONDARY ACCESSION(S): PRJNA148233

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide mapping of histone methylation in human melanocytes and melanoma cell lines

2013-12-01 | E-GEOD-33930 | biostudies-arrayexpress

Whole-genome gene expression profiling of normal melanocytes and melanoma cell lines

2013-09-04 | GSE31909 | GEO

Whole-genome gene expression profiling of normal melanocytes and melanoma cell lines

Project description:Aberrant DNA methylation and histone modifications both contribute to carcinogenesis, but how these two epigenetic factors interact to impact gene expression remain unclear. To address this issue, we studied gene expression profiles, DNA methylation and two key histone modifications (H3K4me3 and H3K27me3), in two normal melanocytes (HEMn and HEMa) and two melanoma cell lines SK-MEL-28 and LOXIMVI. Using these data, we analyzed the relationship between epigenetic factors and gene expression status in both normal and melanoma cells, and the impact of epigenetic switches on gene expression change during melanomagenesis. Each of the two normal melanocytes (HEMn and HEMa) and the two melanoma cell lines SK-MEL-28 and LOXIMVI was cultured in triplicate. For each cell line, the same culture conditions and cell density were applied to the triplicates. Total RNA was extracted and microarray analysis was performed for genome-wide gene expression profiling. Using the Sentrix Human-HT12 v4 Beadchip, all four cell samples, each in triplicate, were examined in 12 individual arrays on a same beadchip. Thus, together with the data on DNA methylation and histone modifications, we could not only analyze the epigenetic regulation of gene expression in each cell sample, but also investigate the expression change associated with epigenetic changes in melanoma when compared to normal melanocytes.

2013-09-04 | E-GEOD-31909 | biostudies-arrayexpress

miRNA profiling of Melanoma Cell lines and Normal Melanocytes

Project description:To identify microRNAs potentially involved in melanomagenesis we compared microRNA transcription profiles between melanoma cell lines and cultured melanocytes.

2011-10-17 | GSE25653 | GEO

Next Generation Sequencing of Transcriptomes of Cutaneous Melanocytes and Metastatic Melanoma Cell Lines (miRNA-Seq)

Project description:The goal of the study is to compare NGS-derived transcriptome (miRNA-seq) profiles of melanocytes and metastatic melanoma cells and identify microRNAs involved in melanomagenesis

2019-01-16 | GSE109244 | GEO

Next Generation Sequencing of Transcriptomes of Cutaneous Melanocytes and Metastatic Melanoma Cell Lines (mRNA-Seq)

Project description:The goal of the study is to compare NGS-derived transcriptome (mRNA-seq) profiles of melanocytes and metastatic melanoma cells and identify genes involved in melanomagenesis

2019-01-16 | GSE109245 | GEO

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.

2024-02-14 | PXD043551 | Pride

DNA methylation analysis by DREAM of UV irradiated melanocytes

Project description:Ultraviolet radiation (UVR) is the greatest risk factor for melanoma development. While the role of UVR in DNA mutagenesis is generally accepted, the role of UVR-induced mutations in melanomagenesis remains controversial. To understand better how UVR is contributing to melanoma development, we investigated the non-mutational effect of UVR on the epigenome, specifically DNA methylation. Aberrant DNA methylation changes are a hallmark in melanoma and there are few reports on the effects of UVR on DNA methylation. We exposed melanocytes to UVR and cultured them for one-month to detect heritable and stable changes in DNA methylation. We found both hyper and hypo methylated sites after UVR exposure. While many of these changes occurred outside of promoters and areas of active gene expression, there were changes in promoter DNA methylation changes that correlated with changes in gene expression. These changes also correlated with those found in melanoma and UVR sensitive sites were prognostic of patient overall survival. Our work shows UVR-induced DNA methylation changes in melanocytes and may be a novel non-mutational mechanism in which UVR contributes to melanoma development.

2024-03-25 | GSE169695 | GEO

miRNA profiling of Melanoma Cell lines and Normal Melanocytes

Project description:To identify microRNAs potentially involved in melanomagenesis we compared microRNA transcription profiles between melanoma cell lines and cultured melanocytes. miRNA microarrays were manufactured by Agilent Technologies (Santa Clara, CA), and contain 20-40 features targeting each of 470 human miRNAs (Agilent design ID 016436). Sequences of the 470 miRNAs were obtained from the Sanger miRBase, release 9.1. Labeling and hybridization of total RNA samples were performed according to the manufacturer’s protocol. 100ng total RNA was used as input into the labeling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C. The labeling and hybridizations of the nine human tissues were done 4-5 times using the same starting RNA sample for each tissue. Total RNA was extracted from 51 melanoma cells and 2 pools of melanocytes using the QIAGEN miRNA kits.

2011-10-16 | E-GEOD-25653 | biostudies-arrayexpress

Quantitative histone mass spectrometry identifies elevated histone H3 lysine 27 trimethylation in melanoma

Project description:Normal cell growth is characterized by a regulated epigenetic program that drives cellular activities such as gene transcription, DNA replication and DNA damage repair. Perturbation of this epigenetic program can lead to events such as mis-regulation of gene transcription and diseases such as cancer. To begin to understand the epigenetic program correlated to the development of melanoma, we performed a quantitative mass spectrometric analysis of histone posttranslational modifications mis-regulated in melanoma cell culture. Aggressive melanoma cells were found to have elevated histone H3 lysine 27 trimethylation (H3K27me3) as well as over-expressed methyltransferase EZH2 that adds the specific modification. The altered epigenetic program that led to elevated H3K27me3 in melanoma cell culture was found to directly silence transcription of the tumor suppressor gene RUNX3. The elevated level of H3K27me3 and silencing of RUNX3 transcription was also validated in advanced stage human melanoma tissues. The study presented underscores the utility of using high resolution mass spectrometry to identify mis-regulated epigenetic programs in diseases such as cancer, which could ultimately lead to the identification of biological markers for diagnostic and prognostic applications.

2016-07-22 | MSV000079979 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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