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Sample GSM1588764 Query DataSets for GSM1588764
Status Public on Sep 15, 2015
Title Pt10-DP3-1
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 10 melanoma, post BRAFi resistance, 3rd 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 0.840894012274009
cg00212031 0.194519317160827
cg00213748 0.524497991967872
cg00214611 0.189435336976321
cg00455876 0.460780410113478
cg01707559 0.235364159555467
cg02004872 0.0665148063781321
cg02011394 0.95893768344627
cg02050847 0.879504753482202
cg02233190 0.0750043305040707
cg02494853 0.0251558212910792
cg02839557 0.173380782918149
cg02842889 0.139818491208168
cg03052502 0.90154028436019
cg03155755 0.867894027840144
cg03244189 0.261341582469801
cg03443143 0.856771152197869
cg03683899 0.0878539296110082
cg03695421 0.540639941154836
cg03706273 0.0397307151908009

Total number of rows: 485512

Table truncated, full table size 13824 Kbytes.

Supplementary file Size Download File type/resource
GSM1588764_9247377060_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588764_9247377060_R05C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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