Dataset features

Specifications


Application: aCGH data analysis
Number of samples: 44
Release date: Apr 27 2011
Last update date: Mar 23 2012
Access: Public
Diseases: Colorectal Neoplasms, Hereditary Nonpolyposis, Neoplasms, Ovarian Neoplasms, Dystonic Disorders, Hereditary Breast and Ovarian Cancer Syndrome
Dataset link Genomic profiling of hereditary epithelial ovarian cancer using tiling resolution array CGH

Experimental Protocol


DNA was extracted from formalin fixed, paraffin embedded tumor tissue according to protocols from the UCSF Waldman Laboratory, San Francisco, CA, USA (http://cc.ucsf.edu/people/waldman/Protocols/paraffin.html), with an additional purification step using Phase Lock Gel tubes (Eppendorf AG, Hamburg, Germany). DNA quality was assessed using a Ready-To-Go RAPD analysis kit (GE Healthcare, Little Chalfont, UK) with primers 5’-AATCGGGCTG-3’ and 5’-GAACGGGTG-3’. PCR products were validated on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Tiling 32k BAC microarrays, with contiguous genome wide coverage, were produced at the Microarray DNA Resource Centre, SCIBLU Genomics, Department of Oncology, Lund University, Sweden (http://www.lth.se/sciblu). Labeling and hybridization were performed in short, 2-8 μg tumor DNA and 2 µg reference DNA (Promega Corporation, Madison, WI, USA) were labeled with Cy3-dCTP and Cy5-dCTP, using BioPrime Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, CA, USA). Tumor and reference DNA were pooled and mixed with Human COT-1 DNA (Invitrogen). Hybridizations were conducted using the MAUI® Hybridization System (BioMicro systems Inc, Salt Lake City, UT, USA) and the slides were scanned in an Agilent Microarray Scanner (Agilent Technologies).

Repositories


GEO

GSE28850

BioProject

PRJNA140677

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Contact


Katarina Bartuma