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Reverse transcription (RT) was done in a reaction component of 20 μl, which contained 2 μl miScript Reverse Transcriptase Mix, 2 μl miScript Nucleics Mix, 4 μl miScript HiSpec Buffer, a certain volume of template RNA containing 100 ng total RNA and a little RNase-free water increasing reaction volume to 20 μl.
Volume of template DNA used (2.0 μL; ~50 ng) worked fine for PCR amplification.
The starting population theoretically represented 760,000 E2 and E6 amplicons, and 28,571 HMBS amplicons per 2 μl of NA6 template (the volume of template loaded in each PCR reaction), which equated to a load of 53 HPV16 copies per diploid genome.
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A recent meta-analysis on NAATs for TB lymphadenitis found that studies which used volumes of template >20 µl were more accurate than studies that used lesser template volumes [17].
After extensive optimization to reduce the volumes of template required and level of background fluorescence, we were unable to detect DNA in any of our extractions.
A volume-of-interest template [15] as implemented in PMOD (PMOD Technologies Ltd ,Zurich, Switzerland) was used to obtain brain time-activity curves.
The surface area and pore volume of the template silica xerogel (H900) were observed to be (240 m2 g−1) and (0.286 ccg−1) respectively.
PCR reactions were performed in 10 μL volumes containing 5 μL PerfeCTa™ SYBR green master mix (2×), 0.3 μL each primer (10 μM; 300 nM final concentration), 1 μL volume of DNA template (1 20 ng), and 3.4 μL of PCR-grade water (Solis BioDyne, Tartu, Estonia).
A 10 μl volume of PCR template was then digested with 5 U BstUI in a total volume of 30 μl for 3 h at 60°C.
In experiment 3, the combination of the number of ligase enzyme units and the volume of DNA template in the ligation mix was evaluated, since a possible higher yield of ligated probe pairs due to a higher concentration of enzyme might be restricted by the availability of DNA template.
Next, the impact of the ligation mix with the concentration of the probes, the added volume of DNA template and the quantity of Taq DNA ligase enzyme, and of the time of initial denaturation of the DNA during the multiplex oligonucleotide ligation was evaluated.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com