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Sample GSM1588774 Query DataSets for GSM1588774
Status Public on Sep 15, 2015
Title Pt10-DP8-1
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 10 melanoma, post BRAFi resistance, 8th 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 0.824398333847578
cg00212031 0.119641934928559
cg00213748 0.499147242751563
cg00214611 0.119306656832012
cg00455876 0.696246050919903
cg01707559 0.156044491353414
cg02004872 0.0551804423748545
cg02011394 0.957953975775021
cg02050847 0.944506663680143
cg02233190 0.0655389248073687
cg02494853 0.0227036705461056
cg02839557 0.0204141149023039
cg02842889 0.0580722070844687
cg03052502 0.964996353786853
cg03155755 0.881515032164894
cg03244189 0.193553534386469
cg03443143 0.903511476053022
cg03683899 0.0640581717451524
cg03695421 0.654353456063922
cg03706273 0.0413415930121044

Total number of rows: 485512

Table truncated, full table size 13828 Kbytes.

Supplementary file Size Download File type/resource
GSM1588774_9247377060_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588774_9247377060_R04C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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