|
Status |
Public on Jul 28, 2009 |
Title |
pleural mesothelioma_9215 |
Sample type |
genomic |
|
|
Source name |
pleural mesothelioma
|
Organism |
Homo sapiens |
Characteristics |
disease state: pleural mesothelioma age: 64 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).
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|
|
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.
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|
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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 |
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