Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors [ATAC-seq]

ABSTRACT: With high genetic heterogeneity in melanoma, understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes, pathways, and epigenetic regions influencing melanoma development. We performed RNA-seq and ATAC-seq on fluorescently-isolated melanocytes and melanoma cells from a zebrafish melanoma model.

ORGANISM(S): Danio rerio

PROVIDER: GSE178802 | GEO | 2022/05/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA-seq]

Project description:With high genetic heterogeneity in melanoma, understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes, pathways, and epigenetic regions influencing melanoma development. We performed RNA-seq and ATAC-seq on fluorescently-isolated melanocytes and melanoma cells from a zebrafish melanoma model.

2022-05-24 | GSE178801 | 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

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

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

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

Melan-a melanocytes and B16 melanoma cells

Project description:This SuperSeries is composed of the following subset Series: GSE11580: Time course RA-treatment of B16 mouse melanoma cells GSE11584: Melan-a mouse melanocytes vs. B16 mouse melanoma cells Keywords: SuperSeries Refer to individual Series

2008-07-31 | E-GEOD-11588 | biostudies-arrayexpress

Genome-wide promoter methylation analysis of human melanocytes and melanoma cell lines

Project description:DNA methylation profiling of human melanocytes and melanoma cell lines. Goal was to identify hypermethylated gene promoters in melanoma Genomic DNA from 4 human melanoma cell lines and normal human epidermal melanocytes was subjected to methylated DNA immunoprecipitation (MeDIP) and hybridized to Agilent's G4489A Human Promoter ChIP-on-Chip Set 244K

2014-08-01 | E-GEOD-53801 | biostudies-arrayexpress

Gene expression in melanocytes and metastases melanoma cells from the pig

Project description:Melanoblastoma-bearing Libechov minipigs (MeLiM) provide an animal model for the study of spontaneous cutaneous melanoma. We compared the serial analysis of gene expression (SAGE) profile between normal skin melanocytes and melanoma cells from a pulmonary metastasis of MeLiM. Keywords: disease state study To minimise the contribution of cells other than melanocytes, we constructed SAGE libraries from a primary culture of melanoma cells derived from a pulmonary melanoma metastasis of a young MeLiM and from a pigmented melanocyte cell line, PigMel, derived from the skin of a healthy Meishan pig.

2008-05-07 | E-GEOD-5982 | biostudies-arrayexpress

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

2013-09-04 | GSE31909 | GEO

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

Project description:Study the RNA expression differences in uveal melanoma cells and normal melanocytes, providing new insights into the tumorgenesis of uveal melanoma.

2021-06-08 | GSE176345 | GEO

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

2013-12-01 | GSE33930 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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