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Sample GSM615480 Query DataSets for GSM615480
Status Public on Jun 03, 2011
Title Colorectal Adenocarinoma 14831
Sample type genomic
 
Source name genomic DNA from colorectal adenocarcinoma 14831
Organism Homo sapiens
Characteristics sample type: Fresh Frozen tissue
disease state: Adenocarcinoma
gender: Female
tumor subsite: Distal
tissue source site: The ontario tumor bank network,Canada
batch: Batch 1
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using Trizol reagent according to the manufacturer’s protocol.
Label Cy5 and Cy3
Label protocol standard Illumina label protocol
 
Hybridization protocol Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k Beadchip using standard Illumina protocol.
Scan protocol Beadchips were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting.
Data processing Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. We masked data point as “NA” for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.05 were also replaced as "NA". Furthermore, probes containing at least one “NA” across the tumor sample set were masked as “NA”. Beta values were normalized to eliminate the batch effects. Briefly, the batch means of beta values were brought closer to the overall mean while retaining the original range of DNA methylation data (0 to 1). We used only the tumor samples to calculate the batch means and overall mean in estimating the scaling factor for each batch.
Beta value was calculated as M/(M+U). Detection P values were obtained using the Z-score formula as previously described (Noushmehr et al., 2010, Cancer Cell). Detection P values that are less than 1.11e-16 are represented as 0.
 
Submission date Nov 01, 2010
Last update date Jun 03, 2011
Contact name Toshinori Hinoue
E-mail(s) thinoue@usc.edu
Phone 323-442-7458
Organization name USC Epigenome Center
Street address 1450 Biggy Street, NRT G511
City Los Angeles
State/province CA
ZIP/Postal code 90033-9601
Country USA
 
Platform ID GPL8490
Series (1)
GSE25062 Genome-scale analysis of aberrant DNA methylation in colorectal cancer

Data table header descriptions
ID_REF
VALUE normalized beta value

Data table
ID_REF VALUE
cg00000292 0.704907565
cg00002426 0.270812046
cg00003994 0.088372072
cg00005847 0.567156458
cg00006414 null
cg00007981 0.025593911
cg00008493 0.958579077
cg00008713 0.028859769
cg00009407 0.060267985
cg00010193 0.550119987
cg00011459 0.924089398
cg00012199 0.01751702
cg00012386 0.01920319
cg00012792 0.015222722
cg00013618 null
cg00014085 0.030543209
cg00014837 null
cg00015770 0.687663029
cg00016968 0.642838341
cg00019495 0.138212899

Total number of rows: 27578

Table truncated, full table size 582 Kbytes.




Supplementary file Size Download File type/resource
GSM615480.txt.gz 409.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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