Genomics

Dataset Information

43

DNA methylation profiling reveals common signatures of tumorigenesis and defines epigenetic prognostic subtypes of canine Diffuse Large B-cell Lymphoma


ABSTRACT: In order to assess methylation profiles of dogs affected by DLBCL, a canine CpG microarray platform was developed. Probe design was carried out by the Agilent bioinformatic support team using proprietary prediction algorithms to locate CpG Islands on C. familiaris draft genome as deposited on Ensembl database (CanFam 3.1) and to design high quality oligo-probes. Microarray probes were selected in order to provide the highest possible coverage of dog genome. CDS regions and CpG islands were given top priority. A total of 170,000 probes (60mers, sense orientation) were designed on both CpG and CDS regions. In details, 102,000 probes were designed targeting a total of 36,807 CpG regions while 68,000 probes were directed against 672 CDS; average base pare tiling was 90 bp. Microarray probes were synthesized in situ using the Agilent non-contact ink-jet technology with a 4 x 180K format. Overall design: Comparative analysis of methylation profiles of lymph nodes from n 37 canine DLBCLc and n 7 control dogs. Enriched-fraction and total gDNA (reference) obtained from 44 lymph node samples (37 cDLBCLs and 7 control dogs) were labelled independently with cyanine 5-deoxyuridine triphosphate (dUTP) and cyanine 3-dUTP, respectively. Sample labeling was performed by using SureTag Complete DNA Labeling Kit (Agilent Technologies) following the manufacturer’s recommendations.

INSTRUMENT(S): AMADID: 71420 Dog Methylation Array

SUBMITTER: Serena Ferraresso  

PROVIDER: GSE94913 | GEO | 2017-11-01

SECONDARY ACCESSION(S): PRJNA375790

REPOSITORIES: GEO

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Publications

DNA methylation profiling reveals common signatures of tumorigenesis and defines epigenetic prognostic subtypes of canine Diffuse Large B-cell Lymphoma.

Ferraresso Serena S   Aricò Arianna A   Sanavia Tiziana T   Da Ros Silvia S   Milan Massimo M   Cascione Luciano L   Comazzi Stefano S   Martini Valeria V   Giantin Mery M   Di Camillo Barbara B   Mazzariol Sandro S   Giannuzzi Diana D   Marconato Laura L   Aresu Luca L  

Scientific reports 20170914 1


Epigenetic deregulation is a hallmark of cancer characterized by frequent acquisition of new DNA methylation in CpG islands. To gain insight into the methylation changes of canine DLBCL, we investigated the DNA methylome in primary DLBCLs in comparison with control lymph nodes by genome-wide CpG microarray. We identified 1,194 target loci showing different methylation levels in tumors compared with controls. The hypermethylated CpG loci included promoter, 5'-UTRs, upstream and exonic regions. In  ...[more]

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