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The immunoprecipitated DNA was quantitated by real-time quantitative PCR using Applied Biosystems 7900HT Fast Real-Time PCR System (Applied Biosystems).
The DNA was quantitated with the ultra sensitive PicoGreen reagent (Invitrogen, CA) and subjected to Immunoslot-blot analysis.
Cellular DNA was quantitated in parallel by amplifying part of the adenosine phosphoribosyl transferase gene (forward primer 5'-GGGGCAAAACCAAAAAAGGA, reverse primer 5'-TGTGTGTGGGGCCTGAGTC, probe 5'-TGCCTAAACACAAGCATCCCTACCTCAA).
The PCR amplification of strong-stop DNA was quantitated using DNA isolated from chronically-infected (HIV-1 strain IIIB) human T cells as a standard, using the VB thymocyte cell line.
Purified DNA was quantitated by spectrophotometry and 50 µl were single stranded by incubation with 10 µl of 0.4 N NaOH for 30 min at room temperature and kept on ice to prevent annealing.
The resulting genomic DNA was quantitated using a Nanodrop and 750ug applied to Infinium II Whole Genome Genotyping HumanHap300 Beadarray chips as per manufacturer's instructions (Illumina, San Diego, CA, USA).
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The migrating DNA is quantitated by staining with ethidium bromide and by measuring the intensity of fluorescence at two fixed positions within the migration pattern using a microscope photometer [ 16, 17].
DNAs were quantitated on 1.5% agarose gels by comparison to Lambda DNA references and normalized for concentration prior to pooling eight-fold.
DNA load was quantitated using cloned DNA and results were normalized with a GAPDH real-time PCR.
The single stranded template DNA (sstDNA) was quantitated, including a functional quantitation to determine the optimal amount of the library to use as input for emulsion-based clonal amplification.
The extent of DNA damage was quantitated by image analysis to produce a tail moment, defined as the product of the percentage DNA in the comet tail and the distance between the means of the head and tail distributions, based on the definition of Olive et al (1990).
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