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Sample GSM1588780 Query DataSets for GSM1588780
Status Public on Sep 15, 2015
Title Pt14-DP1-1
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 14 melanoma, post BRAFi 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 0.512899262899263
cg00212031 0.474341192787795
cg00213748 0.52653399668325
cg00214611 0.478202548625084
cg00455876 0.260462826193993
cg01707559 0.356667630893839
cg02004872 0.309954751131222
cg02011394 0.373776908023483
cg02050847 0.285537700865266
cg02233190 0.356521739130435
cg02494853 0.022359592529202
cg02839557 0.396969696969697
cg02842889 0.281857451403888
cg03052502 0.360995850622407
cg03155755 0.482456140350877
cg03244189 0.2534504391468
cg03443143 0.471153846153846
cg03683899 0.476616915422886
cg03695421 0.363636363636364
cg03706273 0.264918802582665

Total number of rows: 485512

Table truncated, full table size 13802 Kbytes.

Supplementary file Size Download File type/resource
GSM1588780_9702496109_R05C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588780_9702496109_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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