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Sample GSM1588748 Query DataSets for GSM1588748
Status Public on Sep 15, 2015
Title Pt8-DP2-1
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, 2nd 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 0.510191082802548
cg00212031 0.46734693877551
cg00213748 0.426920854997112
cg00214611 0.375
cg00455876 0.172969621822691
cg01707559 0.297620704048977
cg02004872 0.262464183381089
cg02011394 0.335252719129878
cg02050847 0.15450643776824
cg02233190 0.185586734693878
cg02494853 0.0175128634306615
cg02839557 0.439247005134056
cg02842889 0.333333333333333
cg03052502 0.483505154639175
cg03155755 0.40668202764977
cg03244189 0.251069900142653
cg03443143 0.30162703379224
cg03683899 0.259887005649718
cg03695421 0.30694087403599
cg03706273 0.0191207194113907

Total number of rows: 485512

Table truncated, full table size 13840 Kbytes.

Supplementary file Size Download File type/resource
GSM1588748_9257625042_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588748_9257625042_R02C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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