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Series GSE12475 Query DataSets for GSE12475
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
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
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.
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
Submission date Aug 18, 2008
Last update date Mar 20, 2012
Contact name Karolin H Nord
Organization name Lund University
Department Dept of Clinical Genetics
Street address BMC C13
City Lund
ZIP/Postal code SE-22184
Country Sweden
Platforms (1)
GPL7180 LUH Illumina human-6 v2.0 expression beadchip
Samples (17)
GSM313325 Chondrosarcoma_case_2
GSM313326 Chondrosarcoma_case_4
GSM313327 Chondrosarcoma_case_11
This SubSeries is part of SuperSeries:
GSE12532 Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors
BioProject PRJNA114213

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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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