DNA was extracted from the suspended solids after pelleting by centrifugation at 4000 × g for 30 min using the Soil DNA kit (GeneAll, Korea). From these extracts, 10–20 ng of DNA was used for quantification of amoA gene copies using a MiniOpticon real-time PCR detection system (Bio-Rad Laboratories, Hercules, CA) and Opticon Monitor Software version 3.1 (Bio-Rad Laboratories, Hercules, CA). The iQ SYBR Green Supermix (Bio-Rad, USA) and specific PCR primers (Table S4 ) were used for amplification. Dilution series of target DNA sequence were included for every real-time PCR for preparing a standard curve as described previously [25 (link)]. Amplification efficiencies ranged from 87 to 102% (R2 values ≥ 0.98) for AOA amoA genes, and from 85 to 97% (R2 values ≥ 0.98) for AOB amoA genes, respectively.
Opticon monitor software version 3
Manufactured by Bio-Rad
The Opticon Monitor Software version 3.1 is a data analysis software designed for use with Bio-Rad's Opticon real-time PCR detection systems. The software's core function is to facilitate the setup, execution, and analysis of real-time PCR experiments.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using opticon monitor software version 3
1
Quantifying Ammonia-Oxidizing Microbes via qPCR
2
Genotyping of PRDM1, GRIN3A, KCNH8 SNPs
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Samples were genotyped for the PRDM1 (rs10499043 C/T), GRIN3A (rs1535628 G/A) and KCNH8 (rs4973706 T/C) SNPs by combining 5 µL Genotyping Master Mix (Applied Biosystems, Paisley, UK), 4.3 µL H2O, 0.5 µL assay mix (Applied Biosystems), and 0.2 µL of purified DNA (~9 ng), for samples derived from blood and saliva. For DNA derived from buccal swabs, 5 µL Genotyping Master Mix was combined with 3.5 µL H2O, 0.5 µL assay mix, and 1 µL DNA solution (~9 ng DNA). Either a Chromo4 (Bio-Rad, Hertfordshire, UK) or a
StepOnePlus real-time system (Applied Biosystems) was used. Briefly, denaturation began at 95°C for 10 min, with 40 cycles of incubation at 92°C for 15 s before annealing and extension at 60°C for 1 min. Initial genotyping analysis was performed with Opticon Monitor software version 3.1 (Bio-Rad) or StepOnePlus software version 2.3 (Applied Biosystems). All samples were analysed in duplicate and were in 100% agreement.
StepOnePlus real-time system (Applied Biosystems) was used. Briefly, denaturation began at 95°C for 10 min, with 40 cycles of incubation at 92°C for 15 s before annealing and extension at 60°C for 1 min. Initial genotyping analysis was performed with Opticon Monitor software version 3.1 (Bio-Rad) or StepOnePlus software version 2.3 (Applied Biosystems). All samples were analysed in duplicate and were in 100% agreement.
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