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Cells were grown in log phase, trypsinized, counted using an automated cell counter (Cellometer®, Nexcelom Bioscience), and then seeded into 75 cm2 flasks at 5×105 cells per flask (in triplicate).
For treatments, 1 × 106 cells were seeded per 25 cultureture flask in triplicate for each dose and control, and the cells allowed to recover for 48 hours prior to treatment.
Prior to treatment with bile acids or butyrate, cells were trypsinised and seeded at 10 cells per flask, in triplicate, in DMEM (Gibco-BRL, Paisley, Scotland), containing 20% FCS (Sera Laboratories International, Crawley, UK), 2 m M glutamine, 0.2 U ml−1 insulin, 1 μg ml−1 hydrocortisone sodium succinate (Sigma, Poole, UK), 100 U ml−1 penicillin and 100 μg ml−1 streptomycin.
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Fermentation was carried out in shake flasks, in triplicate, for 5 days at 28 °C, 200 rpm.
All experiments were carried out in Erlenmeyer flasks, in triplicate.
MCF-7 cells (1 × 10) were incubated in 25 cm flasks in triplicate.
Cells were diluted serially to appropriate concentrations and plated into 50 ml tissue culture flasks in triplicate for 24 h.
After 100 passages, CMT cells (1 × 10) were seeded into 25-cm tissue culture flasks in triplicate.
One million cells were seeded in T75 flasks in triplicate in the cell growth medium containing 0 µM, 2.5 µM and 5 µM of the DNA methyl transferase inhibitor, decitabine (5-aza-2´-deoxycytidine; Sigma-Aldrich) for 14 d.
Then, 25 µl (1 × 10 bacterial cells/ml) were transferred from the 10th transfer flask to three flasks (in triplicate) containing sterile and fresh MSM plus 1 % (w/v) of different carbon sources, i.e. xylose, xylan (from beechwood) and wheat straw.
In order to determine the fluoride degrading capability, the isolated strains were inoculated in 250-mL conical flasks in triplicates containing LB broth with 20 mg/L fluoride concentration and incubated at 30 °C on a rotary shaker at 120 rpm.
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