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Sample GSM1588761 Query DataSets for GSM1588761
Status Public on Sep 15, 2015
Title Pt10-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 10 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 0.834661448509996
cg00212031 0.109851169383416
cg00213748 0.511566771819138
cg00214611 0.242699289660616
cg00455876 0.707720012527404
cg01707559 0.229630165737859
cg02004872 0.0725469728601253
cg02011394 0.97288444457786
cg02050847 0.94037674037674
cg02233190 0.146337421279417
cg02494853 0.0173113314072563
cg02839557 0.140091116173121
cg02842889 0.0814349775784753
cg03052502 0.968974544644349
cg03155755 0.897442924877354
cg03244189 0.193642490695101
cg03443143 0.872728959391452
cg03683899 0.105376344086022
cg03695421 0.59870365074826
cg03706273 0.0309066932395111

Total number of rows: 485512

Table truncated, full table size 13818 Kbytes.

Supplementary file Size Download File type/resource
GSM1588761_7878191071_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588761_7878191071_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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