|
| Status |
Public on Jan 01, 2016 |
| Title |
Osteosarcoma tumor - 22164 (HD aCGH) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Osteosarcoma tumor
|
| 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 custom made high density array chips containing 34,966 probes. The interested region was 1.5 Mb. The average spatial resolution between the probes was 200bp. 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 |
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 |
GPL7312 |
| Series (2) |
| GSE12788 |
Identification and fine mapping of a novel, recurrent deletion in osteosarcoma |
| GSE12805 |
Osteosarcoma (expression, HD aCGH, aCGH) |
|
