GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588721 Query DataSets for GSM1588721
Status Public on Sep 15, 2015
Title Pt3-DP3-2
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 3 melanoma, post BRAFi resistance, 3rd 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 0.676654740608229
cg00212031 0.372357723577236
cg00213748 0.380368098159509
cg00214611 0.323630136986301
cg00455876 0.18001525553013
cg01707559 0.421758926431824
cg02004872 0.29467680608365
cg02011394 0.622660098522168
cg02050847 0.353568498769483
cg02233190 0.228922091782284
cg02494853 0.0332575858618141
cg02839557 0.531809145129225
cg02842889 0.544117647058823
cg03052502 0.734246824139566
cg03155755 0.468998410174881
cg03244189 0.477316050324056
cg03443143 0.688839848675914
cg03683899 0.34
cg03695421 0.422372227579556
cg03706273 0.0454600338082589

Total number of rows: 485512

Table truncated, full table size 13805 Kbytes.

Supplementary file Size Download File type/resource
GSM1588721_9283265037_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588721_9283265037_R03C01_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