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Sample GSM1588729 Query DataSets for GSM1588729
Status Public on Sep 15, 2015
Title Pt5-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 5 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 0.617842323651452
cg00212031 0.58165420592081
cg00213748 0.449720044792833
cg00214611 0.044769552304477
cg00455876 0.525037885165853
cg01707559 0.0877607788595271
cg02004872 0.0182527769438607
cg02011394 0.74044258866447
cg02050847 0.64608682000157
cg02233190 0.0592785223711409
cg02494853 0.0185505043526323
cg02839557 0.0474357522925393
cg02842889 0.0421499292786421
cg03052502 0.949312388682881
cg03155755 0.725413777395354
cg03244189 0.110734295100092
cg03443143 0.582984287135816
cg03683899 0.0416200074654722
cg03695421 0.583747843708654
cg03706273 0.0351228754121655

Total number of rows: 485512

Table truncated, full table size 13833 Kbytes.

Supplementary file Size Download File type/resource
GSM1588729_8795207119_R01C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588729_8795207119_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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