|
| Status |
Public on Mar 03, 2019 |
| Title |
oropharyngeal squamous cell carcinoma 6 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
oropharynx tumor labeled with Cyanine-3 (green)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: oropharynx tumor
topology: tonsil
gender: male
age: 56
hpv status: HPV 16
tnm staging: T4N0M0
risk stratification (ang's 2012): low
death: Yes
overall survival (months): 67.4426229508197
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
OPSCC samples were macrodissected to guarantee at least 80% of tumor cells for nucleic acids extraction. Total DNA were extracted using Qiagen DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA), following the manufacturer’s recommendations.
|
| Label |
Cy3
|
| Label protocol |
The tumors and reference genomic DNA were differentially labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).
|
| |
|
| Channel 2 |
| Source name |
Reference genomic DNA (Promega)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Reference genomic DNA (Promega)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
OPSCC samples were macrodissected to guarantee at least 80% of tumor cells for nucleic acids extraction. Total DNA were extracted using Qiagen DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA), following the manufacturer’s recommendations.
|
| Label |
Cy5
|
| Label protocol |
The tumors and reference genomic DNA were differentially labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized using the SurePrint G3 Human CGH Microarray 4x180K (Agilent Technologies), following the manufacturer instructions
|
| Scan protocol |
The microarray image analysis was performed using the Agilent Feature Extraction Software v.10.1.1.1 software (Agilent Technologies)
|
| Description |
OSCC6
target sample Cy3-labeled mixed with reference sample Cy5-labeled
|
| Data processing |
Data was processed and quality control filtered using the Feature Extraction v.10.1.1.1 software (Agilent Technologies) and an in-house pipeline
|
| |
|
| Submission date |
Mar 05, 2018 |
| Last update date |
Mar 04, 2019 |
| Contact name |
mateus camargo barros filho |
| E-mail(s) |
mateuscbarros@gmail.com
|
| Organization name |
AC Camargo Cancer Center
|
| Street address |
Tagua Street 440
|
| City |
Sao Paulo |
| State/province |
SP |
| ZIP/Postal code |
05409011 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL10150 |
| Series (2) |
| GSE111393 |
Oncogenic drivers in 11q13 associated with prognosis in advanced oropharyngeal carcinomas (aCGH data set) |
| GSE111395 |
Oncogenic drivers in 11q13 associated with prognosis in advanced oropharyngeal carcinomas |
|
