Total nucleic acids were isolated from tissues by homogenization with extraction reagent (TRIzol; Invitrogen-Gibco, San Diego, CA).
19 20 Pure RNA was prepared by treatment of total nucleic acid preparations with DNase 1 (RQ1; Promega Life Sciences, Madison, WI), followed by phenol-chloroform extraction and ethanol precipitation. RNA preparations were assessed for residual DNA by standard PCR using primers targeting the 18S rRNA gene. cDNA was prepared for qPCR analyses using the M-MLV reverse transcriptase enzyme (Invitrogen-Gibco, Carlsbad, CA) and random hexamers as primers, as described.
9 19 SYBR-green-based qPCR was used to assess relative transcript levels from host genes. These analyses were performed as described by us and others.
9 20 21 22 23 24 The sequences were targeted and the primers used for these studies were generated from GenBank (http://www.ncbi.nlm.nih.gov/Genbank; provided in the public domain by the National Center for Biotechnology Information, Bethesda, MD) with Gene Runner software (Hastings Software, Hastings, NY). Primers used were as follows: for iNOS, 5′ primer, 5′-CAGCTGGGCTGTACAAACCTT-3′ and 3′ primer, 5′-CATTGGAAGTGAAGCGTTTCG-3′ to yield a 95-bp product; for TNF-α, 5′ primer, 5′-CTACTCCCAGGTTCTCTTCAA-3′ and 3′ primer, 5′-GCAGAGAGGAGGTTGACTTTC-3′ to yield a 110-bp product; for 18S rRNA, 5′ primer 5′-CGGCTACCACATCCAAGGAA-3′ and 3′ primer, 5′-GCTGGAATTACCGCGGCT-3′ to yield a 187-bp product; and for actin, 5′ primer, 5′-AGAGGGAAATCGTGCGTGAC-3′ and 3′ primer, 5′-CAATAGTGATGACCTGGCCGT-3′ to yield a 139-bp product.
23 24 Primers were confirmed to amplify the predicted products by testing under qPCR conditions. Each assay typically was repeated twice, with each sample run in duplicate each time. Signals from each sample were normalized to values obtained for the 18S rRNA gene (iNOS) or the β-actin gene (TNF-α), which were run as housekeeping genes simultaneously with the experimental samples. Analyses were performed in a sequence detector (model 7700; Applied Biosystems, Foster City, CA), and data were analyzed using the sequence detection software (ver. 1.7; Applied Biosystems). The results from each run for each mouse were averaged and expressed as the relative level of mRNA transcript. PCR for iNOS and for TNF-α were performed as separate experiments at different times. In the interval between the two sets of experiments, there was a switch from 18S rRNA to β-actin as the housekeeping gene due to the latter’s lower copy number. For quality control purposes, qPCR for TNF-α was performed on a subset of samples using both 18S rRNA and β-actin as the housekeeping gene, and similar results were obtained with the different housekeeping genes (data not shown). Age-matched samples were run for each of the three mouse strains in each run to control for interassay variability.