|
| Status |
Public on Aug 01, 2013 |
| Title |
ovarian cancer cell line ES-2 |
| Sample type |
genomic |
| |
|
| Source name |
human ovarian cancer cell line: ES-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ES-2
originating repository: ATCC
literature reported histotype: clear cell carcinoma
predicted histology: Atypical non-serous carcinoma
|
| Treatment protocol |
None
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Gentra Pure Gene DNA extraction Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Q-Bit fluoremtric assay.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000. The array image was acquired using Affymetrix GeneChip® Command Console.
|
| Description |
hybridized to Affymetrix SNP 6.0
|
| Data processing |
Copy number values for individual SNP and CNV probes were extracted and converted from CEL files into signal intensities using Partek Genomics Suite (v6.6) software.
Copy number data was estimated from signal intensity on Affmetrix SNP 6.0 arrays. Copy number ratio values (ratio of the intensity readings from the raw data file to a control) were generated in Partek Genomics Suite (v 6.6) using a Partek corporation distributed baseline (control) file of normal (2N) genomic DNA and default parameters. Post import values were corrected for localized GC content using the inbuilt Partek feature based on methods described in Diskin et al. (Nucleic Acids Research. 2008. 36:19).
|
| |
|
| Submission date |
Jun 27, 2013 |
| Last update date |
Aug 01, 2013 |
| Contact name |
Michael S Anglesio |
| Organization name |
University of British Columbia
|
| Department |
Obstetrics and Gynecology
|
| Lab |
OVCARE
|
| Street address |
3427-600 W 10th Ave
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z4E6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE48351 |
Affymetrix SNP6 copy number data on ovarian cancer cell lines |
|
