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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 08, 2009 |
| Title |
Osteosarcoma Copy Number Analysis |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes.This a-CGH is a part of an expriment whose aim was to identify, genomic imbalance, DNA methylation and gene expression profiles in a panel osteosarcoma tumors.
Keywords: comparative genomic hybridization
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| Overall design |
The Agilent Human Genome CGH microarray 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for U2OS array-CGH experiments. Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic tumour DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C. Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies). Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy5-dUTP or Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA). Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.
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| Contributor(s) |
Sadikovic B |
| Citation(s) |
19286668 |
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| Submission date |
Sep 17, 2008 |
| Last update date |
Oct 26, 2016 |
| Contact name |
Bekim Sadikovic |
| E-mail(s) |
bsadikov@gmail.com
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| Organization name |
The SickKids Hospital and Princess Margaret Hospital
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| Street address |
555 University Avenue
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1X8 |
| Country |
Canada |
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| Platforms (2) |
| GPL4091 |
Agilent-014693 Human Genome CGH Microarray 244A (Feature number version) |
| GPL9128 |
Agilent-014693 Human Genome CGH Microarray 244A (Probe name version) |
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| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE12885 |
Genome-wide changes in DNA methylation and copy number play a role in deregulation of gene expression in osteosarcoma |
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| Relations |
| BioProject |
PRJNA114179 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12830_RAW.tar |
473.4 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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