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Gene expression levels were quantitated using branched-DNA-technology-based QuantiGene Reagent System (Panomics), according to the manufacturer's protocols.
Cell-associated HIV-1 RNA and DNA levels were quantitated using a previously published method [33] with a limit of detection of 3 coPBMCs106 PBMCs.
Transcript levels were quantitated using the Luminex 200 system (LuminexCorp, Austin, TX) and analyzed using the MasterPlex EX software (Miraibio, San Francisco, CA).
The gel images were digitally recorded and the amplicons levels were quantitated using the computer-assisted image analyzer Gel-Pro (IPS, North Reading, MA).
Total activity levels were quantitated using an Omnitech Digiscan open-field activity monitor (Columbus, Ohio, USA) when the rats were 7 months old.
For real-time PCR analysis, mRNA and 28S rRNA levels were quantitated using a Transcriptor First Strand cDNA Synthesis Kit (Roche), a LightCycler Taqman Master (Roche), and each mRNA (or rRNA) specific primer pair and probe (Table S3).
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Then the mRNA level was quantitated using real-time PCR analysis.
Differences in mRNA levels between samples were quantitated using the standard curve method.
Levels of miRNAs were quantitated using individual miRCURY LNA Universal RT microRNA PCR Assays (Exiqon, Denmark).
S1P levels in dried extracts were quantitated using a whole cell receptor binding assay [59].
Levels of viral RNA were quantitated using an MGB assay against L1 wherein results were normalized to the host mRNA encoding elongation factor 1A (EF1A), using the formula by Pfaffl[11].
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