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Sample GSM1588827 Query DataSets for GSM1588827
Status Public on Sep 15, 2015
Title Pt23-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 23 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 0.888742797478634
cg00212031 0.0718861668222644
cg00213748 0.602622061482821
cg00214611 0.146056082307848
cg00455876 0.754522555530112
cg01707559 0.228862328463922
cg02004872 0.0407832744405183
cg02011394 0.97723725523405
cg02050847 0.951894650065382
cg02233190 0.181176142158264
cg02494853 0.0304148384523335
cg02839557 0.0648395721925134
cg02842889 0.140025173064821
cg03052502 0.962507672073652
cg03155755 0.925362024631209
cg03244189 0.310085836909871
cg03443143 0.898467280813215
cg03683899 0.0836760236009297
cg03695421 0.738312676668841
cg03706273 0.305191467489077

Total number of rows: 485512

Table truncated, full table size 13814 Kbytes.

Supplementary file Size Download File type/resource
GSM1588827_9513149040_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588827_9513149040_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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