E-MTAB-2340 - Comparative genomic hybridization by array of human high grade glioma sample and control DNA using a custom oligonucleotide array

Status
Released on 1 March 2014, last updated on 13 May 2014
Organism
Homo sapiens
Samples (3)
Array (1)
Protocols (4)
Description
Custom oligonucleotide array CGH. We designed two fine-tiling oligonucleotide microarrays to cover the specific amplicons observed at chromosome 2p22.1 and 10q11.21 This was undertaken using the Agilent custom array design tool e-Array (Agilent, Santa Clara, CA, USA; https://earray.chem.agilent.com/), and comprised 700 probes covering 43.56Ð43.70 Mb on chromosome 10 and 5000 probes covering 39Ð40 Mb on chromosome 10 with a median probe interval of 200 bp on 2x105K microarray. Due to limited amount of material, DNA was whole genome amplified (WGA) using the GenomePlex Complete Whole Genome Amplification Kit (Sigma, Gillingham, UK) starting with 10 ng of sample and control DNA, and following the manufacturers protocol. WGA DNA was labelled using the Agilent Genomic DNA ULS labelling kit, hybridised as per manufacturers instructions, and scanned on the Agilent 2505B Microarray Scanner System.
Experiment types
comparative genomic hybridization by array, disease state design
Contact
Citation
The prognostic role of intragenic copy number breakpoints and identification of novel fusion genes in paediatric high grade glioma. Diana Carvalho, Alan Mackay, Lynn Bjerke, Richard G Grundy, Celeste Lopes, Rui M Reis and Chris Jones.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MTAB-2340.idf.txt
Sample and data relationshipE-MTAB-2340.sdrf.txt
Raw data (1)E-MTAB-2340.raw.1.zip
Array designA-MEXP-2379.adf.txt
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