GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588738 Query DataSets for GSM1588738
Status Public on Sep 15, 2015
Title Pt6-DP2-1
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 6 melanoma, post BRAFi resistance, 2nd 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 0.818396406000152
cg00212031 0.629254079254079
cg00213748 0.730332351703828
cg00214611 0.0888272033310201
cg00455876 0.734884626618635
cg01707559 0.129119435477817
cg02004872 0.0361650957822448
cg02011394 0.956040894185224
cg02050847 0.958948253315898
cg02233190 0.654627225519288
cg02494853 0.0409048131218069
cg02839557 0.0845856590811507
cg02842889 0.0974174174174174
cg03052502 0.955749066998401
cg03155755 0.921329539378199
cg03244189 0.395859139975226
cg03443143 0.873049754871953
cg03683899 0.0602309083321742
cg03695421 0.768258859784284
cg03706273 0.038785721481581

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588738_9513149079_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588738_9513149079_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap