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A standard curve for quantifying human DNA was generated using human genomic DNA (Roche Applied Sciences, Indianapolis, IN) with dilutions ranging from 10,000 to 1 pg.
Complementary DNA was generated using iScript (BioRad, Hercules, CA).
The XbaI site in exon 4 of the γ DNA was generated by silent mutation.
For more efficient microarray hybridizations, single stranded DNA was generated from the first PCR amplification.
DNA was generated either in a one-step or in a two-step RT-PCR.
Double stranded DNA was generated by mixing equimolar amounts of the complementary oligonucleotides in annealing buffer (Ambion, CA, USA).
A standard curve derived from serially-diluted reference DNA was generated in order to check PCR efficiency between the plates.
Single-stranded microarray template DNA was generated by reverse transcription of the cRNA in the presence of random hexamers.
Nascent HIV-1 DNA was generated in reactions without added DNase I (Fig. 6, reactions 1 2).
UM.L (universally methylated DNA ) was generated as a positive control by treating normal peripheral blood leukocyte (PBL) DNA with the CpG methylase M.SssI (New England Biolabs) [25].
U2M.L (universally unmethylated DNA) was generated as a negative control by amplifying the same DNA used to generate the positive control DNA using the GenomiPhi kit (GE Healthcare) as described by the manufacturer.
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