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Sample GSM1588834 Query DataSets for GSM1588834
Status Public on Sep 15, 2015
Title M229R5-PLX-2
Sample type genomic
Source name tumor cell line
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 Melanoma cell line M229, BRAFi resistant subline, rep 2
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 0.444289693593315
cg00212031 0.219760479041916
cg00213748 0.396099024756189
cg00214611 0.453326456936565
cg00455876 0.229249011857708
cg01707559 0.421159726721913
cg02004872 0.223382045929019
cg02011394 0.522040614165428
cg02050847 0.342028985507246
cg02233190 0.25
cg02494853 0.0212597927723022
cg02839557 0.364139020537125
cg02842889 0.516292541636495
cg03052502 0.409006499535747
cg03155755 0.503844182470528
cg03244189 0.341388030345603
cg03443143 0.362740497419052
cg03683899 0.232467532467532
cg03695421 0.267764705882353
cg03706273 0.0254510842575732

Total number of rows: 485512

Table truncated, full table size 13813 Kbytes.

Supplementary file Size Download File type/resource
GSM1588834_7878191071_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588834_7878191071_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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