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Series GSE7364 Query DataSets for GSE7364
Status Public on Mar 29, 2007
Title Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data.
Keywords: genomic DNA, CGH, Copy Number Variation
 
Overall design Genomic DNA isolated from peripheral blood samples and from Neuroblastoma cell lines was fragmented by DNAseI and biotin labeled by terminal transferase. Labeled DNAs were hybridized to U133plus2.0 GeneChips (Affymetrix). Hybridization and other conditions were slightly modified from those suggested for 10K Mapping Arrays (Affymetrix) and washing conditions were carried out as suggested for 100K Mapping Arrays. Probe set signals were either generated using the RMA algorithm or using the in-house developed WPP algorithm. Copy-number variation between Neuroblastoma and normal DNA was calculated.
 
Contributor(s) Auer H, Newsom DL, Nowak NJ, McHugh M, Singh S, Yu CY, Yang Y, Wenger GD, Gastier-Foster JM, Kornacker K
Citation(s) 17470268
Submission date Mar 26, 2007
Last update date Mar 25, 2019
Contact name David Lawrence Newsom
E-mail(s) newsomd@ccri.net
Organization name Nationwide Children's Hospital
Department Microbial Pathogenesis
Lab Biomedical Genomics Core
Street address 700 Children's Drive
City Columbus
State/province OH
ZIP/Postal code 43205
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (8)
GSM133533 Neuroblastoma cell line IMR32_graCNV
GSM133534 Peripheral Blood Mononuclear cells (C4_graCNV)
GSM133535 Peripheral Blood Mononuclear cells (C2_graCNV)
Relations
BioProject PRJNA100437

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
GSE7364_RAW.tar 42.5 Mb (http)(custom) TAR (of CEL)

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