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Sample GSM1588767 Query DataSets for GSM1588767
Status Public on Sep 15, 2015
Title Pt10-DP4-2
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, pre MAPKi treatment, 4th 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 0.889213916723719
cg00212031 0.0972027972027972
cg00213748 0.671534653465347
cg00214611 0.130899119642084
cg00455876 0.753235681624428
cg01707559 0.141171653676057
cg02004872 0.0362118723836067
cg02011394 0.969575209772952
cg02050847 0.9466097170315
cg02233190 0.0430823593367763
cg02494853 0.0322064594023544
cg02839557 0.0437464946719013
cg02842889 0.0623808103540215
cg03052502 0.967663853028798
cg03155755 0.920081490104773
cg03244189 0.102120535714286
cg03443143 0.901560468140442
cg03683899 0.0504347826086957
cg03695421 0.686652159822214
cg03706273 0.0273761326392905

Total number of rows: 485512

Table truncated, full table size 13827 Kbytes.

Supplementary file Size Download File type/resource
GSM1588767_9341679010_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588767_9341679010_R06C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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