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After a final precipitation step, all the RNAs were dissolved in nuclease-free water.
The RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1), and a final precipitation with ethanol and sodium acetate [ 44].
Substrates Whey protein concentrate (WPC-80) manufactured from sweet whey and spray dried was provided by Davisco Foods International, Inc. Alpha-s-casein was obtained according to the method of Thompson and Kiddy (1964) by a urea calcium chloride procedure with a final precipitation in ethanol ammonium acetate solution.
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However, the longer reaction times and requirement of additional steps for the final precipitation of tetrabromobisphenol A are the major drawbacks associated with these methods.
Subsequently, 30 mL 1 M oxalic acid solution was heated to boiling with magnetic stirring and added into the above solution slowly under constant stirring to form a final black precipitation, and then cooled by ice-water mixture.
Subsequently, the pools were purified by an additional phenol-chloroform extraction procedure including a final ethanol precipitation, because the pilot studies had also demonstrated that this treatment strongly improves the results of the array analyses.
To summarise, the following principle procedures were followed: Total RNA was isolated from freeze-dried tissues using the Trizol procedure (Chomczynski and Sacchi, 1987) incorporating a final LiCl2 precipitation.
For a final RNA precipitation, 300 μl cold isopropanol and 300 μl of salt solution containing 1.2 M sodium citrate and 0.8 M NaCl were added, samples were incubated at -20°C for 10 min, and centrifuged at 10 000g for 20 min at 4°C.
The DNA was extracted using a modified version of the Cenis method for fungal DNA extraction with an additional step of 1 1 dilution with a solution of 24:1 of chloroform isoamyl alcohol before the final precipitation, to remove remaining impurities [ 57].
Bacterial DNA was extracted from aliquots of feces, and after the final precipitation, DNA was resuspended in 150 µL of TE buffer, and stored at −20°C for further analysis, as previously described [26].
The final precipitation was analysed by Western blotting.
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