GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588842 Query DataSets for GSM1588842
Status Public on Sep 15, 2015
Title SKMel28-DMSO-1
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 SKMel28, parental, MAPKi sensitive in DMSO
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 0.48152634766808
cg00212031 0.42037037037037
cg00213748 0.268175582990398
cg00214611 0.327672955974843
cg00455876 0.257713248638838
cg01707559 0.850188200553164
cg02004872 0.308525033829499
cg02011394 0.453822629969419
cg02050847 0.871209785178333
cg02233190 0.0893464637421665
cg02494853 0.0208037391742657
cg02839557 0.945766062602965
cg02842889 0.057639366827254
cg03052502 0.480431848852901
cg03155755 0.538269550748752
cg03244189 0.225047679593134
cg03443143 0.254116355653128
cg03683899 0.0628342245989305
cg03695421 0.332009531374106
cg03706273 0.0279676817899316

Total number of rows: 485512

Table truncated, full table size 13835 Kbytes.

Supplementary file Size Download File type/resource
GSM1588842_9702496109_R03C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588842_9702496109_R03C02_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