|
| Status |
Public on Mar 21, 2012 |
| Title |
Lung adenocarcinoma 05L45_T (methylation) |
| Sample type |
genomic |
| |
|
| Source name |
Lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: T16
tissue source: nci-edrn
bisulfite plate: 32
beadchip: 6
beadstrip: G
bisulfite alu: 15.09497
age: 39
tissue: Lung tumor
gender: Female
ethnicity: Asian
pack years: 0
smoking status: Never
Stage: Stage IA
recurrence: No
kras mutation status: WT
egfr mutation status: WT
lkb1 mutation status: WT
kras mutation type: WT
subject: 05L45
|
| Treatment protocol |
Bisulfite treatment
|
| Growth protocol |
Fresh-frozen tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted after macrodissection and a proteinase K digstion by phenol-chloroform
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Standard Illumina protocol performed at the USC Epigenome Center
|
| Scan protocol |
Standard Illumina scan protocol performed at the USC Epigenome Center
|
| Data processing |
DNA methylation levels are reported as β-values, calculated from mean non-background corrected methylated (M) and unmethylated (U) signal intensities for each locus for each sample using the formula (β=M/(M+U)) and the Illumina BeadStudio software v3.2. Probes with detection p-values of >0.05 as described previously (Noushemehr et al., 2010) were deemed not significantly different from background noise and were labeled “NA”.
|
| |
|
| Submission date |
Oct 11, 2011 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Ite Laird-Offringa |
| E-mail(s) |
[email protected]
|
| Phone |
(323) 865-0655
|
| Fax |
(323) 865-0158
|
| Organization name |
University of Southern California
|
| Department |
Biochemistry
|
| Lab |
Ite Laird-Offringa
|
| Street address |
1441 Eastlake Avenue, Suite 6420
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE32861 |
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression |
| GSE32867 |
DNA methylation and gene expression in lung adenocarcinoma |
|
