|
| Status |
Public on Sep 01, 2012 |
| Title |
lymph node metastasis patient 055, cancer, Homogenized |
| Sample type |
genomic |
| |
|
| Source name |
surgically resected material
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
source tissue: lower gingiva
Stage: 4a
metastasis: lymph node metastasis
tissue: oral squamous cell carcinoma tumor from lower gingiva
individual: patient 055
|
| Treatment protocol |
Surgically resected tissue was frozen and stored in -80 C freezer. Frozen tissue was manually homogenized prior to extraction of genomic DNA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from surgical materials using the QIAamp DNA Mini Kit (Qiagen) for tumor tissue. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
Using Genome-Wide Human SNP Sty assay kit (Affymetrix), DNA was prepared and was hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip Scanner 3000-7G.
|
| Description |
Hybridized to 250K_Sty
|
| Data processing |
Copy number analysis was performed using Genotyping Console software v4.0 (Affymetrix).
|
| |
|
| Submission date |
Sep 08, 2011 |
| Last update date |
Sep 01, 2012 |
| Contact name |
Ken Miyaguchi |
| E-mail(s) |
[email protected]
|
| Phone |
81-3-5803-4696
|
| Organization name |
Tokyo Medical and Dental University
|
| Lab |
Bioinformatics
|
| Street address |
5-45, Yushima 1, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL3720 |
| Series (1) |
| GSE31984 |
Genome-wide copy number analysis for occult lymph node metastasis in oral squamous cell carcinoma |
|
