|
| Status |
Public on Dec 06, 2012 |
| Title |
Osteosarcoma cell line 143B [copy number] |
| Sample type |
genomic |
| |
|
| Source name |
Osteosarcoma cell line 143B
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 143B
cell type: Osteosarcoma
sample origin: Not available
gender: female
age (yrs): 13
atcc number: CRL-8303
|
| Biomaterial provider |
ATCC
|
| Growth protocol |
The osteosarcoma cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching, Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency. The osteoblast cells were maintained in medium provided by the manufacturer, split when reaching 80 % confluency, and harvested when enough cells for DNA and RNA isolation were obtained.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA).
|
| Label |
Biotin
|
| Label protocol |
Standard Affymetrix label protocol
|
| |
|
| Hybridization protocol |
Standard Affymetrix hyb protocol
|
| Scan protocol |
Standard Affymetrix scan protocol
|
| Description |
Osteosarcoma cell line 143B Affymetrix SNP 6
|
| Data processing |
Quality control was performed using the Genotyping Console v3.0.1 software (Affymetrix), applying the contrast quality control (CQC) algorithm with a minimal call rate of > 86 %. DNA copy number analysis was performed using the Nexus software (BioDiscovery, California, USA), with the SNPRank segmentation algorithm using default settings (threshold of 0.6 for high copy gain, 0.2 for gain, -0.2 for loss and -1.0 for homozygous loss).
|
| |
|
| Submission date |
Feb 22, 2012 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Leonardo A. Meza-Zepeda |
| E-mail(s) |
leonardm@rr-research.no
|
| Organization name |
The Norwegian Radium Hospital
|
| Department |
Dept. of Tumor Biology
|
| Street address |
Ullernchausseen 70
|
| City |
Oslo |
| ZIP/Postal code |
N-0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE36003 |
Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma [DNA copy number] |
| GSE36004 |
Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma. |
|
