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Normalized DNA template was quantified by real-time PCR as described previously (Ammar et al. 2009; Smith et al. 2009), diluted to 8pM, and clusters were generated on a single-read flow cell.
Next-generation sequencing: we used the Illumina HiSeq2000 sequencing platform as described below: Normalized DNA template was quantified by real-time PCR, diluted to 8 pM, and clusters were generated on a single-read flow cell.
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Selected ligation products (chimeric DNA template) are quantified by a subsequent quantitative PCR step.
Copy numbers of the target template were quantified in peripheral blood and peritoneal fluid through generation of standard curves by serial dilution of plasmids for EpCAM and the housekeeping gene β-glucuronidase (GUS) (105 - 101 plasmid copies).
The total RNA templates were quantified by spectrophotometry and subjected to 1.0% formaldehyde denatured agarose gel electrophoresis.
The transcripts of Bmras, the same as Bmrp49, in prepared cDNA templates were quantified on a real-time thermal cycler, LightCycler 480 Real-Time PCR System (Roche Diagnostics, Indianapolis, IN, USA).
It should be noted that an extended mispriming check is required for the 3C method since hybrid templates are quantified.
The cDNA templates were quantified by the QuantiFast™ SYBR Green PCR kit according to the manufacturer's instructions.
Relative template abundance was quantified using the relative standard curve method described in the ABI PRISM 7900HT manual and the data were normalized for the quantity of the β-actin transcript [69].
For samples K27-1, K27-2, and IgG, the initial template DNA was quantified by Nanodrop and Aligent Bioanalyzer.
The intensity of the native target (NT) and template bands was quantified by digital image analysis using Molecular Analist (Biorad, Veenendaal, the Netherlands).
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