|
| Status |
Public on Aug 11, 2016 |
| Title |
OVCA-CellLine-HCC5011CL_SNP6 |
| Sample type |
genomic |
| |
|
| Source name |
OVCA-CellLine
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: cell line
sample source id: HCC5011
gender: Female
cell type: ovarian carcinoma
|
| Treatment protocol |
No treatments were applied
|
| Growth protocol |
Tumour cells were enriched from malignant effusions (OVCA tumour ascites) by two or more cycles of low speed centrifugation plus differential substrate attachment. Cell lines were cultured in ACL4 or RPMI growth media supplemented with 5% FBS. Xenografts were generated by injecting purified tumour cells intraperitoneally into athymic nude mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell pellets using the Qiagen DNeasy Blood and Tissue kit
|
| 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 werewashed and scanned according to manufacturer instructions (Affymetrix)
|
| Description |
HCC5011CL
|
| Data processing |
CHP files were created from CEL file intensities using the Affymetrix Genotyping Console using the BIRDSEED V2 algorithm with default settings. CEL files were imported into Partek Genomics Suite Software with correction for fragment length, GC content, probe sequence. The corrected probe intensities were then quantile normalized. Copy number profiles were generated using Partek's Paired Copy Number Analysis workflow using patient matched constitutional DNA (ie. BloodLine) as a baseline for defining somatic alterations in each OVCA sample (tumour/cell line/xenograft). The Genomic Segmentation algorithm was applied with SNR=0.3, a 30 marker minimum segment size, and p-values < 10-7 for defining copy number alterations (CNAs).
SNP array normalized probe data = UTSWovca_SNP_Feb2015_AllCopyNumber_transpose.txt
|
| |
|
| Submission date |
Jul 29, 2015 |
| Last update date |
Aug 11, 2016 |
| Contact name |
Kelsie L Thu |
| Organization name |
BC Cancer Research Centre
|
| Street address |
675 West 10th Avenue
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE71522 |
Affymetrix SNP array data for Ovarian Cancer Samples |
| GSE71525 |
A comprehensively characterized cell line panel highly representative of clinical ovarian high-grade serous carcinomas |
|
