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To run the assay, add 5 µl of assayed chromatographic fraction to 95 µl of charging mix containing at final concentration in the reaction mix [10 mM PEP; 1 mM ATP; 0.05 mg/ml pyruvate kunase (KP), 0.003 mg/ml myokinase (MK); 5 µM tRNAPhe, 15 µM tRNALeu, 0.2 mM [H] Phe and 0.2 mM [C] Leu, both with specific activity of at least 50 cpm/pmol.
One cannot deselect testing for rifampicin resistance and only run the assay for TB detection, although it is possible for the laboratory to omit results for rifampicin resistance when reporting to the healthcare provider.
In preparation for the assay the 12 ng/μl DNA was plated at 6.6 μl/well (giving a total of 79.2 ng DNA/well) in MicroAmp Optical 96-well reaction plates (Life Technologies); this was done in triplicate to provide each of the three test laboratories with enough DNA to run the assay.
For 40 samples or more (with a maximum of 87 samples per run), the assay should be performed in 2 runs (PCR 1 and PCR 2) using the experimental plate for calibration.
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In addition, no expensive dedicated laboratory equipment is needed to run the assays, and the sequencing library is compatible with any Illumina sequencer.
Cells were grown for 3 to 5 days at 37°C in a humidified 5% CO2 atmosphere, with daily medium changes including a final medium change two hours prior to running the assay.
For running the assay in 1536-well formathethe same protocol as described for APE1 above was followed.
We ran the assay in duplicate for all samples with the exception of 18 serum samples which were measured only once as we were limited by sample volume.
A total of 1 µg uncapped luciferase RNA per 30 µL reaction and added to the RRL master mix just prior to running the assay.
The laboratory staff running the assay was blinded to the disease state of individual samples.
Plasma samples were thawed and centrifuged to remove any precipitates prior to running the assay.
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