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The DNA bands were extracted using a gel extraction kit (QIAquick, QIAGEN Sciences, Germantown, MD, USA) and sequenced directly using a BigDye Terminator Cycle-sequencing kit (ABI PRISM 310NT Genomic Analyzer, Perkin-Elmer Applied Biosystems, Foster, CA, USA).
All visible bands were extracted using Qiagen QIAquick gel extraction kit (Crawley, UK) and sequenced.
Bands were extracted using a razor blade and stored at -20°C until gel extraction was performed.
Identified gel bands were extracted using the PureLink Quick Gel Extraction Kit (Invitrogen) and Sanger sequenced to identify excision products.
Bands were extracted using a QIAquick Gel Extraction Kit microcentrifuge protocol (Qiagen Sciences, Valencia, CA) and sequenced on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA) using Big Dye Terminator v3.1 Cycle Sequencing Kits (Applied Biosystems, Foster City, CA).
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The product band was extracted using a QIAquick gel extraction kit (Qiagen, UK).
Protein gels were either subjected to Western blot analysis using standard methods or stained with SimplyBlue SafeStain Coomassie G-250 stain (Invitrogen) to visualize protein, and gel bands of interest were extracted using a razor blade.
In each band, amplitude envelopes were extracted using half wave rectification, and pitch synchronous oscillations above 30 Hz were removed with a second-order Butterworth filter.
Bands corresponding to mononucleosomal DNA were extracted using a Qiagen gel extraction kit (Qiagen).
Bands corresponding to mono-nucleosomal DNA were extracted using a Qiagen Gel Extraction kit (Qiagen).
Gel bands of 16S amplicons (1,500 bp) were extracted using sterilized blades and purified using the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare, Piscataway, NJ, USA).
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