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Sample GSM1588781 Query DataSets for GSM1588781
Status Public on Sep 15, 2015
Title Pt14-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 14 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 0.394348894348894
cg00212031 0.437409024745269
cg00213748 0.304659498207885
cg00214611 0.43429003021148
cg00455876 0.359715880263825
cg01707559 0.357688338493292
cg02004872 0.329961089494163
cg02011394 0.497230769230769
cg02050847 0.322916666666667
cg02233190 0.260487804878049
cg02494853 0.0236708622956979
cg02839557 0.59984520123839
cg02842889 0.286523216308041
cg03052502 0.444006309148265
cg03155755 0.43860894251242
cg03244189 0.231913455037187
cg03443143 0.369770580296896
cg03683899 0.402416356877323
cg03695421 0.424961715160796
cg03706273 0.206576999806937

Total number of rows: 485512

Table truncated, full table size 13806 Kbytes.

Supplementary file Size Download File type/resource
GSM1588781_9702496159_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588781_9702496159_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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