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Sample GSM1588735 Query DataSets for GSM1588735
Status Public on Sep 15, 2015
Title Pt6-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 6 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 0.837537124872556
cg00212031 0.48993839835729
cg00213748 0.480372914622179
cg00214611 0.127219654585259
cg00455876 0.772527954395966
cg01707559 0.181486131720123
cg02004872 0.0640791332169079
cg02011394 0.960563195352526
cg02050847 0.910511573050273
cg02233190 0.401277275146354
cg02494853 0.0292237442922374
cg02839557 0.113350125944584
cg02842889 0.125577602609405
cg03052502 0.964207415880278
cg03155755 0.898293029871977
cg03244189 0.348502711624617
cg03443143 0.838064317992366
cg03683899 0.129861780777885
cg03695421 0.716754443712969
cg03706273 0.0363865076407007

Total number of rows: 485512

Table truncated, full table size 13823 Kbytes.

Supplementary file Size Download File type/resource
GSM1588735_9513149040_R01C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588735_9513149040_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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