|
| Status |
Public on Jan 01, 2013 |
| Title |
DNA-HNSCC-09 |
| Sample type |
genomic |
| |
|
| Source name |
Pt 9
|
| Organism |
Homo sapiens |
| Characteristics |
sample identifier: Pt 9
sample type: tumor
disease state: HNSCC
|
| Treatment protocol |
human surgical specimens, flash frozen
|
| Growth protocol |
human HNSCC and UPPP surgical samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from all samples by digestion with 50 µg/mL proteinase K (Boehringer, Mannheim, Germany) in the presence of 1\% SDS at 48°C overnight, followed by phenol/chloroform extraction and ethanol precipitation.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Bisulfite conversion of genomic DNA was done with the EZ DNA methylation Kit (Zymo Research, D5002) by following manufacturer's protocol with modifications for Illumina Infinium Methylation Assay in the Johns Hopkins microarray core.
|
| |
|
| Hybridization protocol |
Chip process and data analysis were performed by using reagents provided in the kit and following manufacturer's manual.
|
| Scan protocol |
Data were extracted and summarized using BeadStudio v3.0 software.
|
| Description |
Sample name: 25414_5374669026_A
|
| Data processing |
Data were analyzed in R from Illumina FinalReport files
|
| |
|
| Submission date |
Oct 25, 2011 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Michael F Ochs |
| Organization name |
Johns Hopkins University
|
| Department |
Oncology Biostatistics
|
| Street address |
550 North Broadway, Ste 1103
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE33202 |
Cancer Outlier Gene Profile Sets Elucidate Pathways and Patient-Specific Targets in Head and Neck Squamous Cell Carcinoma [Illumina HumanMethylation] |
| GSE33232 |
Cancer Outlier Gene Profile Sets Elucidate Pathways and Patient-Specific Targets in Head and Neck Squamous Cell Carcinoma |
|
