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Sample GSM1588813 Query DataSets for GSM1588813
Status Public on Sep 15, 2015
Title Pt21-DD-DP1-2
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 21 melanoma, post BRAFi+MEKi 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 0.850482468711187
cg00212031 0.0594864954984995
cg00213748 0.748979591836735
cg00214611 0.042780260877497
cg00455876 0.799956236605505
cg01707559 0.0850704783437152
cg02004872 0.0233423368476083
cg02011394 0.964547413793103
cg02050847 0.933947640372029
cg02233190 0.0617277647299091
cg02494853 0.0312976697701331
cg02839557 0.0331713637836087
cg02842889 0.0622256449749711
cg03052502 0.972933907720213
cg03155755 0.936529608232533
cg03244189 0.188375713544369
cg03443143 0.883382547955344
cg03683899 0.0188763944066617
cg03695421 0.829512006196747
cg03706273 0.045055234198945

Total number of rows: 485512

Table truncated, full table size 13811 Kbytes.

Supplementary file Size Download File type/resource
GSM1588813_9513149040_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588813_9513149040_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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