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Sample GSM1588795 Query DataSets for GSM1588795
Status Public on Sep 15, 2015
Title Pt17-DP1-2
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 17 melanoma, post BRAFi 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 0.385758513931889
cg00212031 0.333519553072626
cg00213748 0.413377926421405
cg00214611 0.380952380952381
cg00455876 0.26705414499847
cg01707559 0.30687724910036
cg02004872 0.275627615062762
cg02011394 0.534653465346535
cg02050847 0.26817826426896
cg02233190 0.262529832935561
cg02494853 0.0342956864827952
cg02839557 0.362768496420048
cg02842889 0.475993377483444
cg03052502 0.349196538936959
cg03155755 0.43546365914787
cg03244189 0.476527331189711
cg03443143 0.396167788710513
cg03683899 0.300072306579899
cg03695421 0.356814701378254
cg03706273 0.0507635821848561

Total number of rows: 485512

Table truncated, full table size 13801 Kbytes.

Supplementary file Size Download File type/resource
GSM1588795_9513149040_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588795_9513149040_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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