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With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation.
Our assay was designed to apply three differentially labelled BAC DNA probes that when hybridized to interphase nuclei would exhibit signal patterns that are consistent with the normal or the inversion locus.
Allele-specific primers tailed with shared universal tag sequences were designed to speed multiplex design and balance the amplification efficiencies of all loci through the use of a single reverse and two differentially labelled allele denoting forward universal primers.
BrdU-containing DNA fragments were enriched by immunoprecipitation and differentially labelled and hybridized to a genomic microarray.
The MeDIP DNA and reference control were differentially labelled using Cy5 and Cy3 respectively, and co-hybridised to a custom miRNA array and the CpG Island promoter plus array from Roche NimbleGen.
Nuclei from unsynchronised cells were sorted into S and G1 phases, and the S and G1 DNAs were differentially labelled and simultaneously hybridized to either a genomic clone array probes (mean size 150 kb) spaced at 1 Mb intervals [7] or a chromosome 6 tile path array of BAC and PAC clones whose midpoints were spaced at 94 kb intervals on average [6].
Quantification was performed by integrating the extracted ion chromatogram of the differentially labelled peptides.
Universal mouse Reference RNA (Agilent) was differentially labelled and hybridized to the tissue or cultured samples.
Differentially labelled RNA samples were mixed and competitively hybridised to microarrays.
Also in this experiment, the target individual and the group were differentially labelled.
Only a few genes are differentially labelled when comparing the two priming methods.
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