|
| Status |
Public on Jul 28, 2009 |
| Title |
pleural mesothelioma_9159 |
| Sample type |
genomic |
| |
|
| Source name |
pleural mesothelioma
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: pleural mesothelioma
age: 58
gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)
|
| Label |
Cy3,Cy5
|
| Label protocol |
DNA was sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).
|
| |
|
| Hybridization protocol |
Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.
Bisulfite-converted DNAs are biotinylated and hybridized to query oligos, and washed. The hybridized oligos are then extended and ligated to create amplifiable templates with methylation-specific primers. The PCR that follows uses fluorescently labeled universal PCR primers.
|
| Scan protocol |
Arrays were imaged using a BeadArray Reader scanner (Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.)
|
| Description |
no additional information
|
| Data processing |
Illumina BeadStudio Methylation software (version 3.2.0) was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level (β) = (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. The β-value provides a continuous measure of levels of DNA methylation in samples, ranging from 0 in the case of completely unmethylated sites to 1 in completely methylated sites. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations.
|
| |
|
| Submission date |
Jun 11, 2009 |
| Last update date |
Apr 13, 2010 |
| Contact name |
Brock Clarke Christensen |
| E-mail(s) |
brock.clarke.christensen@dartmouth.edu
|
| Organization name |
Dartmouth Medical School
|
| Street address |
7650 Remsen
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
| |
|
| Platform ID |
GPL9183 |
| Series (3) |
| GSE16559 |
Lung adenocarcinoma and mesothelioma DNA methylation |
| GSE20989 |
Mesothelioma integrative genomics: DNA methylation |
| GSE21058 |
Integrated profiling reveals a global correlation between epigenetic and genetic alterations in mesothelioma |
|
