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Sample GSM1588775 Query DataSets for GSM1588775
Status Public on Sep 15, 2015
Title Pt10-DP8-2
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, 8th 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 0.88219111296838
cg00212031 0.136102823043378
cg00213748 0.746635730858469
cg00214611 0.142196333733082
cg00455876 0.74289714238656
cg01707559 0.180764191474451
cg02004872 0.0397558701364754
cg02011394 0.961263347788925
cg02050847 0.9568503864202
cg02233190 0.0609855703784372
cg02494853 0.0250155763239875
cg02839557 0.0747260433667522
cg02842889 0.0932161220766296
cg03052502 0.96654849901946
cg03155755 0.922027173259589
cg03244189 0.136185444008863
cg03443143 0.885189078614655
cg03683899 0.0641760680599223
cg03695421 0.587061873098163
cg03706273 0.0300365463682047

Total number of rows: 485512

Table truncated, full table size 13834 Kbytes.

Supplementary file Size Download File type/resource
GSM1588775_9341679010_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588775_9341679010_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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