# Limits of detection and qPCR efficiencies from cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017 # PI: James T. Hollibaugh # Version: 2019-05-08 ========================= qPCR_Parameters Probe Forward_primer Reverse_primer Cycling_conditions Efficiency Limit_of_Detection_template Limit_of_Detection_sample Number_plates_run Reference ------------------------- Bacterial 16S rRNA TM1389F; CTTGTACACACCGCCCGTC BACT1369F; CGGTGAATACGTTCYCGG PROK1492R; GGWTACCTTGTTACGACTT 94 C 2 m 35 cycles of: 94 C 15 s; 56 C 1 m; Acquisition at 56 C 102 9.9 920-7000 3 Suzuki et al. 2000 Thaumarchaeal 16S rRNA TM519AR; TTACCGCGGCGGCTGGCAC GI_334F; AGATGGGTACTGAGACACGGAC GI_554R; CTGTAGGCCCAATAATCATCCT 94 C 2 m 40 cycles of: 94 C 15 s; 59 C 1 m; Acquisition at 59 C 93.3 4.4 420-3200 2 Suzuki et al. 2000 WCA amoA WCA-amoA-P; ACTCCGCCGAACAGTATCA WCA-amoA-F; ACACCAGTTTGGCTWCCDTCAGC WCA-amoA-R; TCAGCCACHGTGATCAAATTG 95 C 10 m 40 cycles of: 95 C 15 s; 56 C 1 m; Acquisition at 56 C 98.4 2.8 270-1100 3 Mosier and Francis 2011 WCB amoA WCB-amoA-P; CCAAAGAATATYAGCGARTG Arch-amoAFB; CATCCRATGTGGATTCCATCDTG WCB-amoA-R; AAYGCAGTTTCTAGYGGATC 95 C 10 m 40 cycles of: 95 C 15 s; 56 C 1 m; Acquisition at 56 C 95.3 8.2 780-3100 5 Mosier and Francis 2011; Beman et al. 2008 Nitrospina 16S rRNA nd NitSSU_130F; GGGTGAGTAACACGTGAATAA NitSSU_282R; TCAGGCCGGCTAAMCA 94 C 15 m 50 cycles of: 84 C 15 s; 57.5 C 15 s; 72 C 30 s; Acquisition at 80 C 92.8 3.8 360-2700 2 Mincer et al. 2007