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Sample GSM1588818 Query DataSets for GSM1588818
Status Public on Sep 15, 2015
Title Pt22-baseline1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 22 melanoma, pre MAPKi treatment, 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 0.467707838992191
cg00212031 0.871082743948019
cg00213748 0.679450757575758
cg00214611 0.0750375939849624
cg00455876 0.295992274263641
cg01707559 0.652073798708924
cg02004872 0.0242216529857538
cg02011394 0.772233251243906
cg02050847 0.95934347903026
cg02233190 0.0337141487576895
cg02494853 0.0257959192355347
cg02839557 0.066193853427896
cg02842889 0.095577967416602
cg03052502 0.904076219347155
cg03155755 0.623729653804842
cg03244189 0.182874494943158
cg03443143 0.495900638991591
cg03683899 0.0494590417310665
cg03695421 0.339235281338258
cg03706273 0.0273853868550143

Total number of rows: 485512

Table truncated, full table size 13811 Kbytes.

Supplementary file Size Download File type/resource
GSM1588818_9283265061_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588818_9283265061_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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