Skip to Content
MilliporeSigma
  • Absence/presence calling in microarray-based CGH experiments with non-model organisms.

Absence/presence calling in microarray-based CGH experiments with non-model organisms.

Nucleic acids research (2014-04-29)
Martijs J Jonker, Wim C de Leeuw, Marino Marinković, Floyd R A Wittink, Han Rauwerda, Oskar Bruning, Wim A Ensink, Ad C Fluit, C H Boel, Mark de Jong, Timo M Breit
ABSTRACT

Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Dimethyl sulfoxide, PCR Reagent
Supelco
Dimethyl sulfoxide, analytical standard
Sigma-Aldrich
Dimethyl sulfoxide, anhydrous, ≥99.9%
Sigma-Aldrich
Dimethyl sulfoxide, sterile-filtered, BioPerformance Certified, meets EP, USP testing specifications, suitable for hybridoma
Sigma-Aldrich
Dimethyl sulfoxide, BioUltra, for molecular biology, ≥99.5% (GC)
Sigma-Aldrich
8-Octanoyloxypyrene-1,3,6-trisulfonic acid trisodium salt, suitable for fluorescence, ≥90% (HPCE)
Sigma-Aldrich
Dimethyl sulfoxide, ≥99.5% (GC), suitable for plant cell culture
Sigma-Aldrich
Dimethyl sulfoxide, for molecular biology
Sigma-Aldrich
Dimethyl sulfoxide, meets EP testing specifications, meets USP testing specifications
Supelco
Dimethyl sulfoxide, for inorganic trace analysis, ≥99.99995% (metals basis)
Sigma-Aldrich
Dimethyl sulfoxide solution, 50 wt. % in H2O
Sigma-Aldrich
Dimethyl sulfoxide, puriss. p.a., dried, ≤0.02% water
Sigma-Aldrich
Dimethyl sulfoxide, Hybri-Max, sterile-filtered, BioReagent, suitable for hybridoma, ≥99.7%
Sigma-Aldrich
Dimethyl sulfoxide, suitable for HPLC, ≥99.7%
USP
Dimethyl sulfoxide, United States Pharmacopeia (USP) Reference Standard
Dimethyl sulfoxide, European Pharmacopoeia (EP) Reference Standard
Sigma-Aldrich
Dimethyl sulfoxide, ReagentPlus®, ≥99.5%
Sigma-Aldrich
Dimethyl sulfoxide, ACS reagent, ≥99.9%
Sigma-Aldrich
Dimethyl sulfoxide, puriss. p.a., ACS reagent, ≥99.9% (GC)
Sigma-Aldrich
Sodium acetate, anhydrous, BioUltra, for luminescence, for molecular biology, ≥99.0% (NT)
Sigma-Aldrich
Sodium acetate solution, BioUltra, for molecular biology, ~3 M in H2O
Sigma-Aldrich
Ammonium acetate, 99.999% trace metals basis
Sigma-Aldrich
Ammonium acetate solution, BioUltra, for molecular biology, ~5 M in H2O
Sigma-Aldrich
Ammonium acetate, BioUltra, for molecular biology, ≥99.0%
Sigma-Aldrich
Sodium acetate, 99.995% trace metals basis
Sigma-Aldrich
Sodium Acetate Anhydrous, >99%, FG
Supelco
Ammonium acetate, LiChropur, eluent additive for LC-MS
Sigma-Aldrich
Ammonium acetate, for molecular biology, ≥98%
Sigma-Aldrich
Ammonium acetate solution, for molecular biology, 7.5 M
Sigma-Aldrich
Ammonium acetate, BioXtra, ≥98%