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Sample GSM1588711 Query DataSets for GSM1588711
Status Public on Sep 15, 2015
Title Pt2-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 2 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 0.854028938505675
cg00212031 0.695855990999438
cg00213748 0.611451942740286
cg00214611 0.339638157894737
cg00455876 0.632204025503188
cg01707559 0.218506288203471
cg02004872 0.0584298090532505
cg02011394 0.960719006079831
cg02050847 0.909988338073122
cg02233190 0.0742832319721981
cg02494853 0.0142879185310909
cg02839557 0.0810205351586808
cg02842889 0.106292517006803
cg03052502 0.929532222445292
cg03155755 0.924876147161537
cg03244189 0.228632990184343
cg03443143 0.866648277886178
cg03683899 0.0670698185816383
cg03695421 0.336646785950961
cg03706273 0.0886165172103223

Total number of rows: 485512

Table truncated, full table size 13798 Kbytes.

Supplementary file Size Download File type/resource
GSM1588711_8795194168_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588711_8795194168_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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