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Protein was extracted from tissue samples of the patient and the controls after homogenization in RIPA buffer with a proteinase inhibitor cocktail (Complete®, Roche-Diagnostics, Basel, Switzerland), 50 µg protein were separated through denaturating SDS-PAGE with the Laemmli system and blotted on nitrocellulose membranes by the semidry method (Biometra, Göttingen, Germany).
Notably, supplementation of the extraction buffer with a proteinase inhibitor cocktail did not prevent proteolysis (Fig. 1B).
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In experiments using whole-cell lysates, cells were lysed in M-PER buffer supplemented with a proteinase inhibitor mix (Roche Applied Science, Indianapolis, IN, USA), and the lysates were incubated with a specific antibody overnight at 4 °C, followed by pull down with protein G-agarose.
In some experiments, the extraction buffer was supplemented with a proteinase inhibitor cocktail (P9599; Sigma Aldrich, St . Louis MO).
The lysis NP-40 buffer was supplemented with a Proteinase Inhibitor Cocktail Tablets (Roche, IN) every time before use.
Then, 100 mg of intestinal tissue was weighed into a 1.5-ml microcentrifuge tube containing 0.5 ml of TE buffer with the proteinase inhibitor Cocktail (Roche, USA).
The cells were collected in ice-cold PBS, and the cell extracts were prepared in RIPA buffer with the proteinase inhibitor cocktail from Sigma (St . Louis MO).
The pellets were resuspended in lysis buffer with added proteinase K (Sigma-Aldrich, USA) and ≤106-μm-diameter glass beads (Sigma-Aldrich, USA).
FFPE tissues (7 tumors) were deparaffinized with xylene, washed with ETOH, and digested with a proteinase K buffer [ 34].
The samples were powdered and decalcified overnight in a 10 M EDTA solution at 37°C, followed by an overnight incubation in a lysis buffer with proteinase K and SDS at 56°C.
When necessary, to ensure maximum tissue lysis, samples were incubated in a lysis buffer with proteinase K at 56°C overnight.
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