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| Status |
Public on Sep 04, 2013 |
| Title |
Whole-genome gene expression profiling of normal melanocytes and melanoma cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Long H, Issa JJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 06, 2011 |
| Last update date |
Aug 13, 2018 |
| Contact name |
HAI LONG |
| E-mail(s) |
longhai021123@gmail.com
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| Phone |
713-834-4296
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| Organization name |
University of Texas MD Anderson Cancer Center
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| Department |
Leukemia
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| Lab |
Issa
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| Street address |
1515 Holcombe Blvd., Unit 425
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA145205 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31909_RAW.tar |
26.2 Mb |
(http)(custom) |
TAR |
| GSE31909_non_normalized.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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