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| Status |
Public on Apr 01, 2009 |
| Title |
Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (Illumina) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Gene expression profiling of 17 fresh frozen chondrosarcoma biopsies using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA). DNA copy number analyses was also performed in these tumors.
Keywords: chondrosarcoma, gene expression profiling, Illumina
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| Overall design |
Samples displaying a tumor content of >70%, as determined from haematoxylin and eosin-stained frozen sections, were analyzed using the Homo sapiens-6 v2 Expression BeadChips (Illumina Inc., San Diego, CA, USA), containing more than 48,000 transcript probes. In samples demonstrating a lower amount of tumor versus normal tissue, macrodissection of tumor material was performed. For each hybridization, 200 ng of total RNA were processed according to the Illumina® TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX, USA), to produce double-stranded cDNA and subsequently to generate biotin-labelled cRNA. Following the manufacturer’s specifications (Illumina), 1.5 µg of the biotin labeled cRNA were hybridized onto the Homo sapiens-6 v2 Expression BeadChips overnight, and subsequently detected with streptavidin-Cy3 using an Illumina® BeadArray Reader. Image analysis was performed using the Illumina® BeadStudio Application Software.
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| Contributor(s) |
Hallor K, Staaf J, Bovée J, Hogendoorn P, Cleton-Jansen A, Knuutila S, Savola S, Brosjö O, Bauer H, VultvonSteyern F, Jonsson K, Skorpil M, Mandahl N, Mertens F |
| Citation(s) |
19336518 |
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| Submission date |
Aug 18, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Karolin H Nord |
| Organization name |
Lund University
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| Department |
Dept of Clinical Genetics
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| Street address |
BMC C13
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| City |
Lund |
| ZIP/Postal code |
SE-22184 |
| Country |
Sweden |
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| Platforms (1) |
| GPL7180 |
LUH Illumina human-6 v2.0 expression beadchip |
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| Samples (17)
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| This SubSeries is part of SuperSeries: |
| GSE12532 |
Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors |
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| Relations |
| BioProject |
PRJNA114213 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12475_RAW.tar |
370.6 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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