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Sample GSM1588837 Query DataSets for GSM1588837
Status Public on Sep 15, 2015
Title M229DDRpoly-PLXAZD-2
Sample type genomic
Source name tumor cell line
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 Melanoma cell line M229, BRAF+MEKi 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 0.463662790697674
cg00212031 0.344947735191638
cg00213748 0.411453744493392
cg00214611 0.438652256834075
cg00455876 0.178703703703704
cg01707559 0.321368948247078
cg02004872 0.253352152434721
cg02011394 0.41745602165088
cg02050847 0.415073115860517
cg02233190 0.268363636363636
cg02494853 0.0240112994350282
cg02839557 0.415266106442577
cg02842889 0.295302013422819
cg03052502 0.249786142001711
cg03155755 0.447829398324448
cg03244189 0.325738916256158
cg03443143 0.461187214611872
cg03683899 0.362521891418564
cg03695421 0.372824631860776
cg03706273 0.0878740417113181

Total number of rows: 485512

Table truncated, full table size 13807 Kbytes.

Supplementary file Size Download File type/resource
GSM1588837_9702496159_R06C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588837_9702496159_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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