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Sample GSM1588803 Query DataSets for GSM1588803
Status Public on Sep 15, 2015
Title Pt19-baseline-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 19 melanoma, pre MAPKi treatment, 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 0.89717549984132
cg00212031 0.0699235502517248
cg00213748 0.498530852105779
cg00214611 0.0826753367394333
cg00455876 0.767643979057592
cg01707559 0.277154415693459
cg02004872 0.0194429847609038
cg02011394 0.964580410845712
cg02050847 0.957774676939878
cg02233190 0.188277668631303
cg02494853 0.0298934336310923
cg02839557 0.275044989409573
cg02842889 0.0660306771417883
cg03052502 0.96818553030034
cg03155755 0.897153769209785
cg03244189 0.11929671233581
cg03443143 0.922425709387106
cg03683899 0.0975292587776333
cg03695421 0.711144427786107
cg03706273 0.0308340977009794

Total number of rows: 485512

Table truncated, full table size 13836 Kbytes.

Supplementary file Size Download File type/resource
GSM1588803_9702496159_R01C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588803_9702496159_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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