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Series GSE169695 Query DataSets for GSE169695
Status Public on Mar 25, 2024
Title DNA methylation analysis by DREAM of UV irradiated melanocytes
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary 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.
 
Overall design Melanocyte cells were UV irradiated with a broad spectrum wave band ( UVA & UVB) for a total dos of 175 J/m2. Cells were cultured for one month before performing digital restriction enzyme analysis of methylation (DREAM). Genomic DNA was digested by SmaI which recognizes unmethylated CpG sites in the sequence CCCGGG and cuts leaving a 5'-GGG signature. Next, digestion by XmaI was performed which can cut methylated CpG sites in the sequence CCCGGG and leaves a 5'-CCGGG signature. High throughput sequencing was used to map these sites to the genome. Methylation ratios were calculated as the total number of XmaI signature reads over the total number of reads for each specific site. Methylation ratios were adjusted for differences in restriction enzyme efficiency based on values from spiked in methylation standards.
 
Contributor(s) Preston-Alp S, Jelinek J, Issa J, Zaidi MR
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Submission date Mar 26, 2021
Last update date Mar 25, 2024
Contact name Jaroslav Jelinek
E-mail(s) jjelinek@coriell.org
Phone 8567579739
Organization name Coriell Institute for Medical Research
Department Research Labs
Street address 403 Haddon Avenue
City Camden
State/province NJ
ZIP/Postal code 08103
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (16)
GSM5212530 HEMnDP1 control1
GSM5212531 HEMnDP1 control2
GSM5212532 HEMnDP1 control3
Relations
BioProject PRJNA717719
SRA SRP312305

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE169695_RAW.tar 42.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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