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Sample GSM1588707 Query DataSets for GSM1588707
Status Public on Sep 15, 2015
Title Pt1-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 1 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 0.880440556716365
cg00212031 0.131176323049912
cg00213748 0.575230852797393
cg00214611 0.224422442244224
cg00455876 0.583290620194772
cg01707559 0.178537398761315
cg02004872 0.0685765309918893
cg02011394 0.970558327493822
cg02050847 0.926556298494654
cg02233190 0.0562965260545906
cg02494853 0.0113469005221583
cg02839557 0.059915164369035
cg02842889 0.131461558646025
cg03052502 0.97336624658958
cg03155755 0.894688644688645
cg03244189 0.206126035651519
cg03443143 0.897907622511635
cg03683899 0.100291167906826
cg03695421 0.579028697571744
cg03706273 0.438717136099126

Total number of rows: 485512

Table truncated, full table size 13836 Kbytes.

Supplementary file Size Download File type/resource
GSM1588707_8795207119_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588707_8795207119_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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