GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588839 Query DataSets for GSM1588839
Status Public on Sep 15, 2015
Title M238-DMSO2D-2
Sample type genomic
Source name tumor cell line
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 M238, parental, MAPKi sensitive in DMSO, 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 0.789027124455972
cg00212031 0.340053990214274
cg00213748 0.116186066091349
cg00214611 0.0618353344768439
cg00455876 0.738536659800107
cg01707559 0.157474020783373
cg02004872 0.0190218294642362
cg02011394 0.965875663723002
cg02050847 0.0746462604678025
cg02233190 0.0306778822365166
cg02494853 0.0193420288342514
cg02839557 0.0413984842137335
cg02842889 0.0406677921590696
cg03052502 0.977265445671876
cg03155755 0.92482924127746
cg03244189 0.105933662343624
cg03443143 0.778226290156186
cg03683899 0.026053138400315
cg03695421 0.127361408907148
cg03706273 0.0169176935950099

Total number of rows: 485512

Table truncated, full table size 13851 Kbytes.

Supplementary file Size Download File type/resource
GSM1588839_8795207135_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588839_8795207135_R04C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap