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Sample GSM1588783 Query DataSets for GSM1588783
Status Public on Sep 15, 2015
Title Pt15-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 15 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 0.595382078064871
cg00212031 0.433403805496829
cg00213748 0.34192882929345
cg00214611 0.550581915846016
cg00455876 0.205198897203623
cg01707559 0.29415784079262
cg02004872 0.377545404512933
cg02011394 0.441037735849057
cg02050847 0.26647564469914
cg02233190 0.25743162901308
cg02494853 0.0380170825657344
cg02839557 0.322056833558863
cg02842889 0.483258928571429
cg03052502 0.660529344073648
cg03155755 0.501284026707756
cg03244189 0.286547433903577
cg03443143 0.414833438089252
cg03683899 0.24051724137931
cg03695421 0.248595505617978
cg03706273 0.104913294797688

Total number of rows: 485512

Table truncated, full table size 13801 Kbytes.

Supplementary file Size Download File type/resource
GSM1588783_9341679003_R01C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588783_9341679003_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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