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Sample GSM1588722 Query DataSets for GSM1588722
Status Public on Sep 15, 2015
Title Pt4-baseline-1
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 4 melanoma, pre MAPKi treatment, 1st biopsy
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 0.813777653318398
cg00212031 0.103912233492031
cg00213748 0.701455711818406
cg00214611 0.0633488205861329
cg00455876 0.746703465194726
cg01707559 0.122699386503067
cg02004872 0.0198492833571393
cg02011394 0.954875842789015
cg02050847 0.911273261085445
cg02233190 0.0234945669949486
cg02494853 0.0258937808943557
cg02839557 0.058648063507337
cg02842889 0.043960884503568
cg03052502 0.973203375863147
cg03155755 0.874450256932549
cg03244189 0.0977195507642296
cg03443143 0.84438921114459
cg03683899 0.0378973105134474
cg03695421 0.651123357354811
cg03706273 0.0625047937513523

Total number of rows: 485512

Table truncated, full table size 13823 Kbytes.

Supplementary file Size Download File type/resource
GSM1588722_9257625042_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588722_9257625042_R06C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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