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Gene expression was determined using the relative quantitation method [66] and Hprt expression was used to normalize all sample template concentrations.
The analysis was performed using the relative quantitation method with PCR efficiency corrections on QBase [11].
All reactions were carried out in triplicate and measurements analyzed using the relative quantitation 2-ΔΔCt method.
Data were normalised using the Relative Quantitation of Gene Expression method as outlined in the ABI 7700 manual.
Relative expression was determined using the relative quantitation method with a standard curve and gene expression was normalised to 18S abundance.
The results were analyzed using the "Relative Quantitation of Gene Expression" method described in ABI Prism 7700 Sequence Detection System User Bulletin #2, Rev B. An initial study comparing only two cell lines, LnCaP and MCF10A, was carried out for the three platforms.
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Relative quantitation of gene expression was performed using the relative standard curve method.
Data analysis was performed using the relative quantitation/comparative CT (△△CT) [ 30].
Data analysis was performed by the StepOne Software Applied Biosystemss) using the Relative Quantitation/Comparative CT (ΔΔCT) setting.
To determine HER2 gene amplification, the ΔCt was determined (average Ct value of the target gene minus the average Ct value of the reference gene) and used to calculate the ΔΔCt for each DNA sample, using the mean relative quantitation (RQ) value derived from a panel of 49 normal lymphocyte DNA samples (RQ=1.003±0.086) as the experimental calibrator.
Chromatograms from Sialidase S digestions for Tri-2SA, Tri-3SA, and Tri-4SA fractions by SRM detection; diagrams depicting the glycan linkage/branching isomers; tables of SRM transitions for sialidase S digestion of fetuin N-glycan studies and the p-values obtained from independent two-tailed Student's t-test of the difference between the relative quantitation using UV and SRM detection.
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