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Sample GSM1588819 Query DataSets for GSM1588819
Status Public on Sep 15, 2015
Title Pt22-baseline1-2
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, 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 0.467218799722574
cg00212031 0.889689774574235
cg00213748 0.584677419354839
cg00214611 0.10394862036156
cg00455876 0.38394611282627
cg01707559 0.657745753988677
cg02004872 0.0246378869639307
cg02011394 0.75156904706242
cg02050847 0.885418619474335
cg02233190 0.0516204152920629
cg02494853 0.0230578097327588
cg02839557 0.0572819168850618
cg02842889 0.0813609467455621
cg03052502 0.927049559981473
cg03155755 0.663729391699829
cg03244189 0.219844916714532
cg03443143 0.497710779437676
cg03683899 0.0635270201592411
cg03695421 0.502799680036567
cg03706273 0.0286689961880559

Total number of rows: 485512

Table truncated, full table size 13797 Kbytes.

Supplementary file Size Download File type/resource
GSM1588819_9283265037_R03C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588819_9283265037_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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