|
| Status |
Public on Jan 01, 2016 |
| Title |
Osteosarcoma tumor - 25044 (aCGH) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Osteosarcoma tumor (aCGH)
|
| Organism |
Homo sapiens |
| Characteristics |
Sample type: osteosarcoma tumor
|
| Growth protocol |
Commercially available osteosarcoma cell lines were grown according to the supplier’s recommendations.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using a standard proteinase K digestion followed by phenol/chloroform/isoamyl alcohol extraction, precipitated with 3M sodium acetate (pH 5.2) and 100% ethanol. The pellet was washed with 70% ethanol and resuspended in TE.
|
| Label |
Cy5
|
| Label protocol |
3 μg of digested DNAs from samples and references were differentially labeled with dUTP-Cy5 and dUTP-Cy3 respectively in a random primer reaction
|
| |
|
| Channel 2 |
| Source name |
genomic DNA from Promega
|
| Organism |
Homo sapiens |
| Characteristics |
Sample type: DNA reference
|
| Growth protocol |
Commercially available osteosarcoma cell lines were grown according to the supplier’s recommendations.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using a standard proteinase K digestion followed by phenol/chloroform/isoamyl alcohol extraction, precipitated with 3M sodium acetate (pH 5.2) and 100% ethanol. The pellet was washed with 70% ethanol and resuspended in TE.
|
| Label |
Cy3
|
| Label protocol |
3 μg of digested DNAs from samples and references were differentially labeled with dUTP-Cy5 and dUTP-Cy3 respectively in a random primer reaction
|
| |
|
| |
| Hybridization protocol |
Reference and experimental samples DNA were co-hybridized on the high-resolution genome wide arrays containing 105,000 oligonucleotide probes. The average spatial resolution between the probes was 21.7 KB . The hybridization was carried out for 40h at 65°C.
|
| Scan protocol |
After washing, the slides were scanned on a laser-based microarray scanner (Agilent) using a resolution of 5 μm
|
| Description |
High molecular weight DNA
Tumor sampls were obtained from the tissues bank at the Laboratory of Oncology Research of the Rizzoli Orthopaedic Institute, Bologna, Italy
|
| Data processing |
aCGH data were extracted (not normalized) using the default procedure in Agilent's Feature Extraction Software and visualized using Agilent CGH Analytics 3.4.27 software
|
| |
|
| Submission date |
Sep 15, 2008 |
| Last update date |
Jan 01, 2016 |
| Contact name |
Yuelin Jack Zhu |
| E-mail(s) |
[email protected]
|
| Phone |
(240)760-7439
|
| Organization name |
NCI
|
| Department |
Genetics Branch, Center for Cancer Research
|
| Lab |
Dr. Paul Meltzer's Lab
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL4093 |
| Series (2) |
| GSE12789 |
High-resolution profiling of copy-number aberrations in osteosarcoma |
| GSE12805 |
Osteosarcoma (expression, HD aCGH, aCGH) |
|
