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Sample GSM320821 Query DataSets for GSM320821
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)

Data table header descriptions
ID_REF
VALUE log(REDsignal/GREENsignal) per feature (processed signals used) representing test/reference

Data table
ID_REF VALUE
1 0.016808923
2 0
3 0
4 0.067038589
5 0.143203193
6 -0.069546602
7 -0.114037174
8 -0.132248461
9 0.037045244
10 -0.08767191
11 -0.016246602
12 0.278073366
13 0.398746857
14 0.07096436
15 -0.423652012
16 -0.079178969
17 0.277349331
18 -0.394926459
19 0.038224236
20 0.489312108

Total number of rows: 104702

Table truncated, full table size 1862 Kbytes.




Supplementary file Size Download File type/resource
GSM320821.txt.gz 28.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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