|
| Status |
Public on Sep 22, 2015 |
| Title |
SCC Sample S17 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Lung Squamous Cell Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
age: 65
gender: M
time (month): 22
event (1=dead; 0=alive): 1
cell type: squamous cell carcinoma
tissue type: lung
|
| Treatment protocol |
Tumor cells were scraped using a scalpel and then collected under the direction of pathologists from ten 10-μm thick FFPE slides for each histological lesion.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from the tumor cells using a DNeasy Blood & Tissue Kit (Qiagen Inc., Hilden, Germany).
|
| Label |
Cy5
|
| Label protocol |
Tumor and reference gDNA (Promega Inc., WI) were labeled with Cy5 and Cy3, respectively, using the Agilent Genomic DNA USL Labeling Kit (Agilent Technologies) for FFPE Samples according to the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Human genomic DNA: Male (Promega)
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Male (Promega)
|
| Treatment protocol |
Tumor cells were scraped using a scalpel and then collected under the direction of pathologists from ten 10-μm thick FFPE slides for each histological lesion.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from the tumor cells using a DNeasy Blood & Tissue Kit (Qiagen Inc., Hilden, Germany).
|
| Label |
Cy3
|
| Label protocol |
Tumor and reference gDNA (Promega Inc., WI) were labeled with Cy5 and Cy3, respectively, using the Agilent Genomic DNA USL Labeling Kit (Agilent Technologies) for FFPE Samples according to the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
A total of 500ng of both gDNA samples and human Cot-I DNA was dissolved in the hybridization mixture supplied within the Agilent Oligo array-CGH Hybridization Kit (Agilent Technologies). After denaturation at 95℃ for 3 minutes and incubation at 37℃ for 30 minutes, the mixtures were slowly dispensed onto the gasket. A microarray slide was then placed onto the gasket slide. The samples were hybridized in a hybridization oven at 65℃ and 20 rpm for 40 hours.
|
| Scan protocol |
Slides were scanned with the Agilent Scanner System, and the Feature Extraction 12.0 (Agilent Technologies) was used for data extraction.
|
| Data processing |
Data were normalized with quantile method with limma package in R (version 2.12.0).
|
| |
|
| Submission date |
Dec 23, 2012 |
| Last update date |
Sep 22, 2015 |
| Contact name |
Dongmei Lin |
| Organization name |
Cancer Hospital, CAMS
|
| Department |
Pathology
|
| Street address |
Panjiayuannanli 17, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100021 |
| Country |
China |
| |
|
| Platform ID |
GPL8841 |
| Series (1) |
| GSE43131 |
Genomic copy number aberrations in primary lung squamous cell carcinoma |
|
