DNase I. The 30–100 bp fragments resulting from DNAse treatments were end-labeled using terminal deoxynucleotidyl transferase and biotinylated dideoxynucleotides and hybridized to the appropriate Sty I or Nsp I early access Mendel® microarrays (Affymetrix, Santa Clara, CA). Arrays were stained, washed and scanned as described (Affymetrix Genechip Mapping Assay Manual) using immunopure strepavidin (Pierce, Milwaukee, WI), biotinylated antistreptavidin antibody (Vector Labs, Burlingame, CA) and R-phycoerythrin strepavidin (Molecular Probes, Eugene, OR). Fluorescence intensities were quantitated using an Affymetrix array scanner as described [21].
