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Sample GSM1588737 Query DataSets for GSM1588737
Status Public on Sep 15, 2015
Title Pt6-DP1-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi
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, post BRAFi resistance, 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 0.872751705602646
cg00212031 0.311914384412183
cg00213748 0.68827678871347
cg00214611 0.0523798679116374
cg00455876 0.812381852551985
cg01707559 0.0982675376313547
cg02004872 0.0487004794347716
cg02011394 0.973052517888484
cg02050847 0.928631363043073
cg02233190 0.371133482864744
cg02494853 0.0266700695463536
cg02839557 0.0740557275541796
cg02842889 0.102056698165648
cg03052502 0.971412321139915
cg03155755 0.939681482714611
cg03244189 0.309052333804809
cg03443143 0.882860693116289
cg03683899 0.0683348151911597
cg03695421 0.725
cg03706273 0.0551506145244536

Total number of rows: 485512

Table truncated, full table size 13813 Kbytes.

Supplementary file Size Download File type/resource
GSM1588737_9513149040_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588737_9513149040_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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