Genomics

Dataset Information

27

Osteosarcoma Copy Number Analysis


ABSTRACT: Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes.This a-CGH is a part of an expriment whose aim was to identify, genomic imbalance, DNA methylation and gene expression profiles in a panel osteosarcoma tumors. Keywords: comparative genomic hybridization Overall design: The Agilent Human Genome CGH microarray 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for U2OS array-CGH experiments. Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic tumour DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C. Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies). Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy5-dUTP or Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA). Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.

INSTRUMENT(S): Agilent-014693 Human Genome CGH Microarray 244A (Feature number version)

SUBMITTER: Bekim Sadikovic  

PROVIDER: GSE12830 | GEO | 2009-09-08

SECONDARY ACCESSION(S): PRJNA114179

REPOSITORIES: GEO

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Publications

Identification of interactive networks of gene expression associated with osteosarcoma oncogenesis by integrated molecular profiling.

Sadikovic Bekim B   Yoshimoto Maisa M   Chilton-MacNeill Susan S   Thorner Paul P   Squire Jeremy A JA   Zielenska Maria M  

Human molecular genetics 20090313 11


Altered gene expression in tumors can be caused by copy number alterations to DNA or mutation affecting coding or regulatory regions of genes. However, epigenetic events may also influence gene expression. Malignant cells can show major disruptions in DNA methylation profiles, which are manifested as aberrant hypermethylation or as hypomethylation of gene promoters, as well as global genomic hypomethylation. In this study we performed integrative whole-genome analysis of DNA copy number, promote  ...[more]

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