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Sample GSM1588805 Query DataSets for GSM1588805
Status Public on Sep 15, 2015
Title Pt19-DD-DP1-2
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 19 melanoma, post BRAFi+MEKi 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 0.875256064690027
cg00212031 0.144150417827298
cg00213748 0.441176470588235
cg00214611 0.473639455782313
cg00455876 0.492782909930716
cg01707559 0.315866887295459
cg02004872 0.145346534653465
cg02011394 0.92888873136268
cg02050847 0.812248995983936
cg02233190 0.218549580661075
cg02494853 0.0164415736934821
cg02839557 0.41488857278331
cg02842889 0.192920353982301
cg03052502 0.893802400131514
cg03155755 0.753938248267171
cg03244189 0.237238697131745
cg03443143 0.86190894268155
cg03683899 0.28739800543971
cg03695421 0.409967845659164
cg03706273 0.0842996502852936

Total number of rows: 485512

Table truncated, full table size 13905 Kbytes.

Supplementary file Size Download File type/resource
GSM1588805_9702496159_R02C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588805_9702496159_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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