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Genomic DNA from strain RM4018 was used as a reference DNA and competitively hybridized with genomic DNA from each of the other A. butzleri strains.
In all cases the genome of Red Jungle Fowl sequence [ 1] was used as a reference DNA.
The remaining 50 μl of the start-sample were stored at −20°C as a reference DNA sample.
Transposable-related sequences were identified using CENSOR online (with default sensitivity parameters and Arabidopsis thaliana as a reference DNA source) [ 68].
The main inclusion criteria were the presence of matching non-malignant normal tissue DNA from the same patient to be used as a reference DNA for the aCGH.
We further used P. falciparum gyrase as a reference DNA metabolic enzyme to show that ACF inhibits the topological activity of this enzyme, possibly by interacting with the substrate DNA.
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We performed comparative genomic hybridization based on microarrays (array-CGH) in a commercial whole-genome 180 K platform containing 180,000 oligonucleotide probes (design 30864, Agilent Technologies, Palo Alto, California) using as reference DNA a commercially available human pool of healthy individuals (Promega).
Adenovirus genome copy numbers were determined using serial dilutions of an adenoviral reference DNA as a standard.
Adenovirus genome copy numbers were calculated by using serial dilutions of an adenoviral reference DNA as a standard.
In the microarray experiments described below, DNA from the T. whipplei Twist strain was used as a reference, whereas the DNA from other isolates was referred as test DNA.
A third MAC DNA preparation was used as the reference DNA in each of these two-color hybridizations.
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