|
Status |
Public on Jan 01, 2016 |
Title |
Osteosarcoma cell line - HUO9N2 (aCGH) |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Osteosarcoma cell line (aCGH)
|
Organism |
Homo sapiens |
Characteristics |
Sample type: cell line
|
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) |
|