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Sample GSM1588746 Query DataSets for GSM1588746
Status Public on Sep 15, 2015
Title Pt8-DP1-1
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 8 melanoma, post BRAFi resistance, 1st biopsy
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 0.517123287671233
cg00212031 0.347921225382932
cg00213748 0.362244897959184
cg00214611 0.360072926162261
cg00455876 0.213387699626232
cg01707559 0.250985392997913
cg02004872 0.227472527472527
cg02011394 0.423099245502031
cg02050847 0.24174653887114
cg02233190 0.218181818181818
cg02494853 0.0161731134047137
cg02839557 0.380460683081811
cg02842889 0.424189143690846
cg03052502 0.293577981651376
cg03155755 0.459899749373434
cg03244189 0.269230769230769
cg03443143 0.391611925214755
cg03683899 0.324392288348701
cg03695421 0.21301775147929
cg03706273 0.0170645237532498

Total number of rows: 485512

Table truncated, full table size 13843 Kbytes.

Supplementary file Size Download File type/resource
GSM1588746_9257625042_R01C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588746_9257625042_R01C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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