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Sample GSM1588776 Query DataSets for GSM1588776
Status Public on Sep 15, 2015
Title Pt10-DP9-1
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, 9th 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 0.851230578853293
cg00212031 0.29852563235493
cg00213748 0.351551644279759
cg00214611 0.158560695927244
cg00455876 0.646733661219225
cg01707559 0.156037791555949
cg02004872 0.0391665993701042
cg02011394 0.953909069040173
cg02050847 0.905721524954334
cg02233190 0.0587104833285289
cg02494853 0.0164633961807342
cg02839557 0.0858272670081783
cg02842889 0.101707228478024
cg03052502 0.949184705474196
cg03155755 0.897898287493513
cg03244189 0.189490445859873
cg03443143 0.887875919129567
cg03683899 0.0385196374622356
cg03695421 0.59102041250945
cg03706273 0.0210562857017977

Total number of rows: 485512

Table truncated, full table size 13832 Kbytes.

Supplementary file Size Download File type/resource
GSM1588776_9247377060_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588776_9247377060_R05C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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