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Before drug application, to acquire a stable baseline, RA-differentiated SH-SY5Y cells were perfused with buffer solution for 5 min and for 25 min with buffer solution to control, and for 25 min for other drugs dissolved in buffer solution.
After electrophoresis, the native-PAGE was washed in 20 mM phosphate buffer (pH 8.0) at 4°C and 50 rpm for 90 min, with buffer changes every 30 min.
The column bound material was recovered by elution for 8 min with buffer B at 1 ml/min.
three times for 5 min with buffer changes, biotinylated goat anti-rabbit antibody (Dako; Glostrup, Denmark) diluted to 1∶400 in TBS was applied for 30 min at room temperature.
The excess dye was washed out for 5 min with buffer.
After washing, samples were permeabilized for 15 min with buffer containing saponin (50 mm Tris, 200 mm NaCl, and 0.05% saponin, pH7.5) at room temperature.
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After hybridization, arrays were washed at room temperature for 2 minutes with Stringent Wash Buffer, 2 mins with Wash Buffer I, 1 min with Wash Buffer II, and 15 seconds with Wash Buffer III (Nimblegen).
After an overnight incubation IP beads were washed 4× for 10 min with wash buffer (10% lysis buffer/dilution buffer), 2× 10 min TE and eluted in 2× 75 μl elution buffer (1% SDS, 0.1 M NaHCO3).
Membranes were washed 4 times, 20 min each with antibody incubation buffer then incubated with the appropriate secondary antibodies (BioRad) diluted 1∶10000 in Buffer A for 2 hr at RT then washed 4×20 min each with Buffer A and once for 5 min with PBS.
Agarose beads were washed twice for 4 min with sonication buffer, twice for 4 min with wash buffer A (sonication buffer with 500 mM NaCl), twice for 4 min with wash buffer B (20 mM Tris-HCl, pH 8.0, 1 mM EDTA, à.25 M LiCl, à.5% NP-40, 0.5% Na-deoxycholate), and finally with Tris-EDTA (TE, pH 8.0).
Microarrays were washed using the GE washing buffers (Agilent Technologies) for 5 min with wash buffer 1 at room temperature followed by 1 min with wash buffer 2 at 37°C.
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