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The current and voltage to the probes and the sample were independently measured and controlled using an Agilent B1500A semiconductor device analyser (Santa Clara, CA, USA).
Three replicate assays for each sample were independently processed.
After further quality trimming and vector contamination removal, the sequences of each sample were independently assembled using phrap (http://www.phrap.org).
A total of 27 replicates of the mock sample were independently PCR-amplified and sequenced with an average of approximately 33,000 reads per replicate sample.
The HPV sequence detected in primary cervical tumour sample were independently validated by directed sequencing in T1094, the only sample with sufficient quality DNA (as shown in Supplementary Figure 1).
For Figure 2, Figure 3C and Figure 1 figure supplement 3, both read counts and enrichment values for each sample were independently scaled by dividing the values at each base by the maximum value encountered among the displayed genes or gene groups across stages after normalizing for both read count and fragment size differences.
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Each sample was independently tested by three times.
The forensic sample was evaluated by a single observer while the archaeological sample was independently scored by three different observers.
The RNA sample was independently prepared for each of the three replications.
All samples were randomized in the experiment and each sample was independently processed in triplicate for the entire experiment to control for potential technical bias.
RNA from each diluted sample was independently extracted using the Ambion MagMax® Viral RNA Isolation kit (Applied Biosystems/Ambion, Austin, TX) and using the Qiagen QIAamp® MinElute Virus Spin kit (Valencia, CA).
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