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After 3 days, cells were lysed as described above and 1 mg protein was precipitated using one volume of TCA.
The samples were then centrifuged (30 min, 13 000 rpm) and the RNA was precipitated from the supernatant overnight using one volume LiCl 4 M. RNA pellets were then washed with 70% ethanol and resuspended in distilled water.
Nucleic acids were precipitated by addition of 130 μl, 10 M ammonium acetate, using one volume of isopropanol.
Nucleic acids were precipitated by addition of 130 μl of 10 M ammonium acetate, using one volume of isopropanol.
Three rounds of depletion for 20 min at 22°C were performed using one volume of pre-cleared HSS mixed with 0.2 volumes of the antibody-bound sepharose.
DNA was extracted using one volume 25:24:1 phenol chloroform:isoamylalcohol mix and centrifuged for 5 min at 10,000 g and 4 °C.
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The solvents adsorbed to the resin packed in the glass columns were desorbed in a fixed-bed mode using one bed volume of 85% (v/v) methanol.
Five elution fractions were collected each using one resin volume of elution buffer (1 mM HEPES pH 7.0, 0.1% PEG, 0.001% CHAPS, 0.1 mM DTT, 200 ng/ μl FLAG peptide (Sigma)).
Promoter regions cloned from genomic DNA prepared from VCaP cells using a high salt extraction buffer (10 m M Tris, pH 7.5, 400 m M NaCl, 100 m M EDTA, 0.6% SDS), protein precipitated with 6 M NaCl before precipitation of DNA using one sample volume of 100% ethanol.
Bound protein was eluted using one resin-bed volume of Elution Buffer (50 mM sodium phosphate, 500 mM sodium chloride, 150 mM imidazole; pH 7.4).
Real-time PCR reactions were performed in triplicate in 20 μl reaction volumes using One Step SYBR PrimeScript RT-PCR Kit II (TaKaRa) according to manufacturer instructions and carried out in the Step One Plus Real-Time PCR thermocycler (Applied Biosystems, USA).
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