|
| Status |
Public on May 17, 2012 |
| Title |
tumor 66 [MSNP] |
| Sample type |
genomic |
| |
|
| Source name |
lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
disease state: adenocarcinoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using Qiagen’s QIAamp DNA minikit and Affymetrix DNA prep instructions using the StyI restriction enzyme digestion. These samples were then additionally digested by HpaII, a methylation sensitive restriction enzyme, following the MSNP protocol (Yuan et al, PMID: 16585166).
|
| Label |
biotin
|
| Label protocol |
Followed Affymetrix instructions.
|
| |
|
| Hybridization protocol |
Followed Affymetrix instructions.
|
| Scan protocol |
Arrays were scanned using the Affmetrix Gene Chip Scanner.
|
| Data processing |
The DNA specimens in this dataset were additionally digested by HpaII restriction enzyme, which is methylation sensitive. These samples were concurrently analyzed with their StyI-only digested counterpart, which are contained in GSE36363 identified with the same Sample Name [see 'Affiliated with' link below]. All CEL files were processed by CRMAv2 (Bengtsson, et al. PMID: 19535535) and sample-wise median centered using control probes (those in a fragment without a HpaII binding site). For probes in fragments having a HpaII binding site, methylation values were calculated using the StyI-only digestion and the StyI+HpaII digestion arrays for each sample. The methylation normalized values were calculated as (StyI - StyI+HpaII)/StyI to give a relative estimate of methylation percentage. These values are given in the data table below.
Note that methylation values are given only for 'methylation sensitive' probesets that measure DNA fragments with a HpaII binding site - those that are methylation sensitive. Methylation sensitive probesets were identified by searching for the HpaII binding site in the StyI digested DNA. For more information on probeset classification, see Yuan et al. (PMID: 16585166). Control site probes have null values in the data table below.
|
| |
|
| Submission date |
Mar 12, 2012 |
| Last update date |
May 17, 2012 |
| Contact name |
Matthew D Wilkerson |
| E-mail(s) |
[email protected]
|
| Phone |
919-966-3864
|
| Fax |
919-966-8212
|
| URL |
http://cancer.unc.edu/nhayes
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Lineberger Comprehensive Cancer Center
|
| Lab |
D. Neil Hayes
|
| Street address |
450 West Drive
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7295 |
| Country |
USA |
| |
|
| Platform ID |
GPL3720 |
| Series (2) |
| GSE36438 |
Human lung adenocarcinoma DNA methylation profiling by MSNP |
| GSE36471 |
Human lung adenocarcinoma |
|
| Relations |
| Affiliated with |
GSM889676 |
