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Sample GSM1588709 Query DataSets for GSM1588709
Status Public on Sep 15, 2015
Title Pt2-baseline-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
Extracted molecule genomic DNA
Extraction protocol genomic DNA
Label Cy5 and Cy3
Label protocol Not provided
Hybridization protocol Not provided
Scan protocol Not provided
Description Patient 2 melanoma, pre MAPKi treatment, 1st biopsy, replicate
Data processing To identify the differentially methylated CpG sites, we analyze the Illumina 450K Methylation array output data using R-package minfi (Aryee et al., 2014). Raw image IDAT files were loaded into the R statistical computing environment using minfi, and the data was normalized using the SWAN function. This output a matrix of methylation indices (beta values), which were continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site. For each site, the methylation change was measured by the percent methylation difference (Δbeta) from paired baseline to DP/DD-DP samples. Minfi function dmpFinder was then applied to calculate the p-value of the logit transformed differential methylation. The p-values were corrected for multiple hypothesis testing with false discovery rates (FDR) q-values. We then used a cutoff of q-value ≤ 0.05 to define differential methylation
Submission date Jan 22, 2015
Last update date Sep 22, 2015
Contact name Willy Hugo
Organization name UCLA
Department Medicine
Street address 10833 Le Conte Ave, 52-121 CHS, Division of Dermatology
City Los Angeles
State/province California
ZIP/Postal code 90095
Country USA
Platform ID GPL13534
Series (2)
GSE65183 Methylation changes in pre MAPKi treatment and post MAPKi resistance Melanomas
GSE65186 Non-genomic and Immune Evolution in Melanoma with Acquired MAPKi Resistance

Data table header descriptions
VALUE Average Beta

Data table
cg00050873 0.831192962649355
cg00212031 0.873988525158288
cg00213748 0.731681034482759
cg00214611 0.0854390110888929
cg00455876 0.747479081742115
cg01707559 0.08723259762309
cg02004872 0.0254565476736717
cg02011394 0.970474207417502
cg02050847 0.951410891089109
cg02233190 0.0371246468230501
cg02494853 0.0200970138561984
cg02839557 0.0354908893119391
cg02842889 0.0400170648464164
cg03052502 0.968096037693291
cg03155755 0.929656066851054
cg03244189 0.100136705399863
cg03443143 0.829970619312442
cg03683899 0.0302350874257509
cg03695421 0.318253106526722
cg03706273 0.440623732480058

Total number of rows: 485512

Table truncated, full table size 13808 Kbytes.

Supplementary file Size Download File type/resource
GSM1588709_8795194168_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588709_8795194168_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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