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Sample GSM1588744 Query DataSets for GSM1588744
Status Public on Sep 15, 2015
Title Pt8-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 8 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 0.472315124489038
cg00212031 0.409953822473063
cg00213748 0.494266055045872
cg00214611 0.42719614921781
cg00455876 0.165316950572466
cg01707559 0.376768161112443
cg02004872 0.197048611111111
cg02011394 0.630983692793267
cg02050847 0.387846961740435
cg02233190 0.185041551246537
cg02494853 0.0172092783852812
cg02839557 0.46468213925328
cg02842889 0.379123584441162
cg03052502 0.430555555555556
cg03155755 0.57411028549081
cg03244189 0.307235621521336
cg03443143 0.44011780104712
cg03683899 0.246130030959752
cg03695421 0.36241610738255
cg03706273 0.0209846978122336

Total number of rows: 485512

Table truncated, full table size 13830 Kbytes.

Supplementary file Size Download File type/resource
GSM1588744_9247377060_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588744_9247377060_R06C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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