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The 700 g pellets were combined, adjusted to 1 M sucrose in HOMO buffer and layered on 1.2 M sucrose in HOMO buffer.
The membrane pellet was then resuspended in STE buffer and layered on top of a continuous gradient composed of 20 60% (wt/wt) sucrose in 5 ml of TE buffer (10 mM Tris-HCl [pH 7.6], 10 mM EDTA).
The pellet was homogenized in 0.25 M STEAKM buffer (Fraction 3, crude nuclear fraction), supplemented with two volumes of 2.3 M STEAKM buffer, and layered on top of 10 ml of 2.5 M STEAKM and centrifuged for 1 h at 124 000g.
143B cells were lysed in lysis buffer and layered on a 2 ml 10%30%% (w/v) sucrose gradient as previously described (Richter et al., 2010).
The pellet obtained was resuspended after overnight incubation in TN buffer and layered on a 10 to 50% (w/w), sucrose gradient for centrifugation at 200,000 g for 6 h.
To separate MAM and mitochondria, the MAM-enriched mitochondrial pellet was resuspended in isolation buffer and layered on top of a self-forming 30% Percoll gradient (225 m m mannitol, 1 m m EGTA, 0.05% BSA, 30% Percoll, 25 m m Na-HEPES pH 7.4).
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The heavy membrane fraction was resuspended in buffer-C and layered on top of a discontinuous sucrose gradient consisting of 1.2 M sucrose in 10 mM Hepes (pH 7.5), 1 mM EDTA, and 0.1% BSA on top of 1.6 M sucrose in 10 mM Hepes, (pH 7.5), 1 mM EDTA, and 0.1% BSA.
The crude synaptosomes were resuspended in 13% (final concentration) Ficoll 400 (in buffer A) and layered on the bottom of a discontinuous gradient, composed by buffer A and 7% Ficoll (in buffer A).
In brief, 20 μl of blood sample was mixed with 80 μl of 0.5% low-melting-point agarose (LMPA) prepared in Ca++- and Mg++-free phosphate buffered saline (PBS) and layered on one end of a frosted glass slide, which was pre-coated with a layer of 200 μl of 1% normal agarose in PBS.
Extracts were diluted after 45 min with dilution buffer (30% glycerol, 0.5% Triton ×100 in BRB80 (80 mM PIPES, 1 mM MgCl2, 1 mM EGTA, pH 6.8)), fixed with fixation buffer (dilution buffer with 4% formaldehyde) and layered on top of a 3 ml cushion (40% glycerol in BRB80).
Buffy coats were collected, washed in 1X Dulbecco's phosphate buffer saline (D-PBS), and layered on top of a 58% percoll gradient (Sigma-Aldrich, St . Louis MO).
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