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Sample GSM1588812 Query DataSets for GSM1588812
Status Public on Sep 15, 2015
Title Pt21-DD-DP1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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 21 melanoma, post BRAFi+MEKi resistance, 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 0.872692927040753
cg00212031 0.0629882551167055
cg00213748 0.766269477543538
cg00214611 0.0680661079345187
cg00455876 0.783364193134881
cg01707559 0.0838167038437349
cg02004872 0.0357610689022793
cg02011394 0.956993816323564
cg02050847 0.960876847394423
cg02233190 0.0626037776033635
cg02494853 0.030234438156831
cg02839557 0.0497617787188989
cg02842889 0.0624163437830222
cg03052502 0.974229339304262
cg03155755 0.917700843448445
cg03244189 0.169320321862695
cg03443143 0.873182485390644
cg03683899 0.0506169928475988
cg03695421 0.829784469691502
cg03706273 0.0347723118107666

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588812_9513149079_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588812_9513149079_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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