SSU rRNA Gene Bacteria V6 amplification of sample: NZS_0002_2007_04_13
Genomic Bacteria DNA of the SSU rRNA gene V6 hypervariable region was amplified using forward primers 967F (CTAACCGANGAACCTYACC, CNACGCGAAGAACCTTANC, CAACGCGAAAAACCTTACC, CAACGCGCAGAACCTTACC, ATACGCGARGAACCTTACC) and reverse primers 1046R (CGACAGCCATGCANCACCT, CGACGGCCATGCANCACCT, CGACGACCATGCANCACCT, CGACAACCATGCANCACCT). We generated PCR amplicons in triplicate 30 uL reaction volumes with an amplification cocktail containing 1.0 U Platinum Taq Hi-Fidelity Polymerase (Invitrogen, Carlsbad, CA), 1X Hi-Fidelity buffer, 200 uM dNTP PurePeak DNA polymerase Mix (Pierce Nucleic Acid Technologies, Milwaukee, WI), 1.5 mM MgSO4 and 0.2 uM of each primer. We added a total of 10 ng template DNA to each PCR reaction and ran a negative, no-template control for each primer pair.  Amplification conditions described in Sogin et al., 2006 were modified as follows: the initial 94C, 3 minute denaturation step was followed by 30 cycles of 94C for 30s, 57C for 60s, and 72C for 90s before a final 10 minute extension at 72C.  The triplicate PCR products were pooled after amplification, purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in 12 uL of Qiagen buffer EB following the manufacturer's protocol.  We assessed the quality, size and concentration of PCR products on a Bioanalyzer 2100 (Agilent, Palo Alto, CA) using a DNA 1000 Lab Chip.