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Sample GSM1588758 Query DataSets for GSM1588758
Status Public on Sep 15, 2015
Title Pt10-baseline2-1
Sample type genomic
 
Source name tumor biopsy
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 Patient 10 melanoma, pre MAPKi treatment, 1st biopsy
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
E-mail(s) hwilly@mednet.ucla.edu
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
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00050873 0.851629969656889
cg00212031 0.157925751325869
cg00213748 0.696047569080098
cg00214611 0.149544072948328
cg00455876 0.639076347670542
cg01707559 0.189771197846568
cg02004872 0.0425282182599763
cg02011394 0.969769072252555
cg02050847 0.950285032480445
cg02233190 0.112977740445191
cg02494853 0.0226829092580713
cg02839557 0.0670900261486739
cg02842889 0.0959010054137664
cg03052502 0.971244354032341
cg03155755 0.878345759802607
cg03244189 0.133779671332928
cg03443143 0.90869938698787
cg03683899 0.08816660179058
cg03695421 0.535002318034307
cg03706273 0.0247332832456799

Total number of rows: 485512

Table truncated, full table size 13818 Kbytes.




Supplementary file Size Download File type/resource
GSM1588758_7878191071_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588758_7878191071_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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