GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588836 Query DataSets for GSM1588836
Status Public on Sep 15, 2015
Title M229DDRpoly-PLXAZD-1
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
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 0.431090790333116
cg00212031 0.444444444444444
cg00213748 0.374853801169591
cg00214611 0.49208083014746
cg00455876 0.306482364156339
cg01707559 0.338149665732154
cg02004872 0.253281853281853
cg02011394 0.406662476429918
cg02050847 0.377859103385178
cg02233190 0.329523809523809
cg02494853 0.0274873444670483
cg02839557 0.519274376417234
cg02842889 0.450261780104712
cg03052502 0.335548172757475
cg03155755 0.406423718344657
cg03244189 0.265807243707796
cg03443143 0.359070464767616
cg03683899 0.342833193629505
cg03695421 0.277524429967427
cg03706273 0.102353038995593

Total number of rows: 485512

Table truncated, full table size 13813 Kbytes.

Supplementary file Size Download File type/resource
GSM1588836_9702496109_R06C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588836_9702496109_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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