Enrichment ratios were examined by qPCR (ABI Prism 7000) with primer sets directed against internal gene body positions of the indicated genes versus a negative position at a gene desert on chromosome 12.
To determine in how far storage time and conditions affect usefulness of RNA isolated from FFPE material, one-step RT-PCR amplification was performed with primer sets directed against the rat HPRT gene, producing amplicons of different lengths from about 100 to 1100 nucleotides.
We performed quantitative RT-PCR experiments with primer sets directed to the last exon or 3′ UTR (Fig. 5A).
We obtained separate siRNA sets directed against transcription factors AP2, NF-1and SP1 and tested the silencing efficiency of each siRNA separately (Supplemental Fig. 1).
Copy number of pPHP611 plasmid [ 17] in each reaction was estimated by using the normalization primer sets directed to the β-lactamase gene responsible for Ampr in the plasmid.
To test the specificity of the AAV PCR systems, different PCR primer sets directed towards pan-AAV, AAV-2 (nested or non-nested) and HPV amplification were tested on DNA from HA-16 cells (contain HPV 18 and AAV-2), SiHa cells (contain HPV 16) and HeLa cells (contain HPV18).
