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Agarose gels (0.8%, 12 cm) cast in 10 mM sodium phosphate buffer were run for 2 hours at 100 volts with the buffer recirculated by a peristaltic pump.
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A sample of the peptide dissolved directly in the loading buffer was run for comparison with material that had been extracted from the air water interface.
NuPAGE Bis-Tris Gels (4% to 12%; Invitrogen) in 3- N-morpholino propanesulfonic acid buffer were run at 175 V for 1.5 hours, and proteins were transferred at 3- N-morpholino propanesulfoniclidene fluoride membranes.
Two no-template-control replicates (buffer blanks) were run for each amplification protocol, and the results were equivalent to background microarray intensities.
PCR products were separated on 1.6% agarose gels (TBE buffer) that were run for 225 minutes at 100 V. Several DNA size standards were run on every gel to aid identification of the target bands.
Strips were overlaid with 0.5% Agarose-LE (Affymatrix, Santa Clara, CA, USA) in 1 × running buffer containing bromphenol blue and were run for 14 16 h (2 W per gel, overnight) at 16°C in an Ettan DALT six electrophoresis system (GE Healthcare).
For the temperature profile, the reaction was set up using 50 mM 2- N-morpholino)ethanesulfonic acid (MES) buffer pH 6.5, and reactions were run for 15 to 60 minutes, depending on enzyme activity, at 5° increments from 45 to 99°C.
After three washings with lysis buffer, 50 μl of 2 × loading buffer was added to each sample and samples were run for SDS-PAGE for 3 h.
Gels were run for 60 min at 180 V in 1× NUPAGE MES SDS running buffer (Invitrogen #NP0002) in the presence of NuPAGE antioxidant (Invitrogen #NP0005).
Gels were run for 50 min at 170 V in 2- N-morpholino)ethanesulfonic acid (MES) running buffer.
The lower chamber was then replenished with fresh buffer and the gel was run for an additional 45 minutes.
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