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Sample GSM1588779 Query DataSets for GSM1588779
Status Public on Sep 15, 2015
Title Pt14-baseline-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 14 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
E-mail(s) hwilly@mednet.ucla.edu
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
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00050873 0.366149979053205
cg00212031 0.3665791776028
cg00213748 0.399596367305752
cg00214611 0.273996509598604
cg00455876 0.298436142484796
cg01707559 0.300572330767713
cg02004872 0.25811209439528
cg02011394 0.3801949717804
cg02050847 0.385061171925306
cg02233190 0.262385321100917
cg02494853 0.0202061955940281
cg02839557 0.362167300380228
cg02842889 0.318901795142555
cg03052502 0.513317191283293
cg03155755 0.289982425307557
cg03244189 0.217037037037037
cg03443143 0.378681045209457
cg03683899 0.258196721311475
cg03695421 0.362540192926045
cg03706273 0.322776108763175

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.




Supplementary file Size Download File type/resource
GSM1588779_9702496159_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588779_9702496159_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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