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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.

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE94913 | GEO | 2017/11/01

SECONDARY ACCESSION(S): PRJNA375790

REPOSITORIES: GEO

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Project description:A genome wide microarray, covering the 10546 presently known and predicted CDS, has been constructed with the Agilent in-situ synthesized 60-mers technology. 1) A library of 10 oligonucleotides per CDS has been design by the manufacturer. 2) A computational step has been performed to determine 3' position, intron position and cross-hybridization rate of all probes. These data have been compiled to attribute a score to each probe and thus, to select a first set of 4 oligonucleotides per CDS. 3) Microarray v.2 (GPL10115), manufactured with this design, have been used for a selection procedure based on the use of transcriptomic experimental data generated with diverse culture conditions. To maximize the number of expressed CDS, experimental data were generated with a large range of growth conditions covering crucial physiological changes from key steps of vegetative growth and sexual development.For each condition, four biological replicates were done to increase the statistical power of the analysis. An oligonucleotide scoring has been settled to select the best oligonucleotide per CDS. The final array design, Microarray v.3 (GPL10116), contained 10,539 probes for nuclear CDS. The array was enriched with 17 mitochondrial CDS probes that did not undergo the experimental screening. Each probe was replicated four times on each 44K array to improve the statistical significance of results. Before using in industrious transcriptomic experiment, ultimate qualification steps have been carried out. First, DNA extracted from the/ S/ and /s /strains was hybridized with the final design Microarray v.III. The apha_ORF and /het/ genes were identified as polymorphic between /s/ and /S/ strains (|FC|>2; a/ =/0.001) confirming previous genetic and molecular analyses (Turcq B etal.,1990*,* /Current genetics, /Sellem et al., 1990, Mol. Gen. Genet.). In second qualification step, a self-to-self hybridization experiment, replicated three times, has been /per/formed with a commonreference: 89.3% of the probes displayed a signal-to-standard-deviation ratio >3. The final microarray design is referenced as AMADID 018343. Microarray slides are available to the research community from Agilent.

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

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