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Sample GSM1588751 Query DataSets for GSM1588751
Status Public on Sep 15, 2015
Title Pt8-DP3-2
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 8 melanoma, post BRAFi resistance, 3rd 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 0.556848228450555
cg00212031 0.44029484029484
cg00213748 0.322010869565217
cg00214611 0.386636636636637
cg00455876 0.193499238191976
cg01707559 0.30937629078893
cg02004872 0.162779628748215
cg02011394 0.603932584269663
cg02050847 0.282220131702728
cg02233190 0.218379446640316
cg02494853 0.0217700258397933
cg02839557 0.446273433927755
cg02842889 0.469521410579345
cg03052502 0.372918492550394
cg03155755 0.499443413729128
cg03244189 0.364188163884674
cg03443143 0.493499308437068
cg03683899 0.231907894736842
cg03695421 0.245989304812834
cg03706273 0.0205622192377159

Total number of rows: 485512

Table truncated, full table size 13827 Kbytes.

Supplementary file Size Download File type/resource
GSM1588751_9341679003_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588751_9341679003_R03C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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