|
| Status |
Public on Jun 03, 2011 |
| Title |
Colorectal Adenocarinoma 14905 |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from colorectal adenocarcinoma 14905
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Fresh Frozen tissue
disease state: Adenocarcinoma
gender: Male
tumor subsite: Rectum
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 |
|
