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Sample GSM1588828 Query DataSets for GSM1588828
Status Public on Sep 15, 2015
Title Pt23-DD-DP1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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 23 melanoma, post BRAFi+MEKi resistance, 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 0.876063567962872
cg00212031 0.0980169386490395
cg00213748 0.658015267175573
cg00214611 0.123336291038154
cg00455876 0.781323662737987
cg01707559 0.146498278678959
cg02004872 0.0290611028315946
cg02011394 0.969526781295987
cg02050847 0.944590703712568
cg02233190 0.197065095968315
cg02494853 0.0320825621178978
cg02839557 0.0845862838296634
cg02842889 0.0995383939038687
cg03052502 0.966963295709777
cg03155755 0.902089989350373
cg03244189 0.231773283160865
cg03443143 0.883826726877404
cg03683899 0.0688600782778865
cg03695421 0.760234959060164
cg03706273 0.170578600098464

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588828_9513149079_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588828_9513149079_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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