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Differential gene expression of zebrafish melanocytes and melanomas [RNA-seq]

ABSTRACT: We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas.

ORGANISM(S): Danio rerio

PROVIDER: GSE83343 | GEO | 2018/02/14

REPOSITORIES: GEO

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Differential gene expression of zebrafish melanocytes and melanomas (microarray)

Project description:We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas.

2018-02-14 | GSE83399 | GEO

methylation analysis in melanomas and melanocytes from the same patient

Project description:DNA methylation is considered the primary epigenetic mechanism underlying the development of malignant melanoma. Since DNA methylation can be influenced by environmental factors, it is preferable to compare cancer and normal cells from the same patient. Here, we employed a novel epidermal sheet cultivation technique to isolate normal melanocytes from unaffected sites of melanoma patients and compared the methylation status with melanoma tissues from the same individuals. We also analyzed primary and metastatic melanoma samples, three commercially available melanocytes, and four melanoma cell lines. Cluster analysis of DNA methylation data classified freshly isolated melanomas and melanocytes into the same group, whereas the four melanoma cell lines were clustered together in a distant clade. Moreover, our analysis discovered methylation at several novel loci (KRTCAP3, AGAP2, ZNF490), in addition to those identified in previous studies (COL1A2, GPX3); however, the latter two were not observed in fresh melanoma samples. Subsequent studies revealed that NPM2 was hypermethylated and downregulated in melanomas, which was consistent with previous reports and indicated that NPM2 immunoreactivity could be used to differentiate melanomas from normal melanocytes or benign disease. Our results highlight the importance of using matched fresh melanoma and melanocyte samples in epigenetic studies. Illumina Infinium 450k Human Methylation Beadchip

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expression analysis in melanomas and melanocytes from the same patient

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Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. II

Project description:Spotted oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged. Six melanoma cultures and two melanocyte cultures. The melanoma cultures are considered, for the purposes of this investigation, replicates from the point of view that they are all melanomas. Three of the melanomas were replicated once or twice in addition.

2010-07-01 | E-GEOD-4576 | biostudies-arrayexpress

Differential gene expression of human melanoma cells [RNA-seq]

Project description:We report the gene expression comparison of human A375 melanoma cells with GDF6 and BMP pathway modulation. These comparisons were used to determine the gene signature regulated by GDF6.

2018-02-14 | GSE83342 | GEO

Differential gene expression of human melanoma cells [ChIP-seq]

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Analysis in melanomas and melanocytes from the same patient

Project description:Analysis in melanomas and melanocytes from the same patient

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methylation analysis in melanomas and melanocytes from the same patient

Project description:methylation analysis in melanomas and melanocytes from the same patient

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expression analysis in melanomas and melanocytes from the same patient

Project description:expression analysis in melanomas and melanocytes from the same patient

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Single cell human melanocytes

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