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Sample GSM1588835 Query DataSets for GSM1588835
Status Public on Sep 15, 2015
Title M229R5-PLX-3
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 3
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 0.429691583899634
cg00212031 0.458834857968223
cg00213748 0.422834193918531
cg00214611 0.484698914116486
cg00455876 0.108381502890173
cg01707559 0.470060670007913
cg02004872 0.226190476190476
cg02011394 0.47612551159618
cg02050847 0.356102003642987
cg02233190 0.301957129543336
cg02494853 0.019556367233573
cg02839557 0.330529857022708
cg02842889 0.440513744930149
cg03052502 0.497087378640777
cg03155755 0.528205128205128
cg03244189 0.350293542074364
cg03443143 0.517985611510791
cg03683899 0.200349956255468
cg03695421 0.329720479178551
cg03706273 0.0311869985599671

Total number of rows: 485512

Table truncated, full table size 13809 Kbytes.

Supplementary file Size Download File type/resource
GSM1588835_7878191071_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588835_7878191071_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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