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RNA preparations were treated with RNase-free DNase RQ1 (Promega Corporation, USA) and resuspended in DEPC-treated water.
The RNA preparations were treated with RNase-free DNase before their use in the reverse transcription.
To eliminate traces of co-extracted DNA all preparations were treated with up to 0.5 units of DNase I per microgram of RNA prior to further reactions.
Subsequently, RNA preparations were treated with DNAse I and re-purified with the RNeasy minicolumn elution kit from QIAGEN according to the manufacturer's instructions.
Preparations were treated next with 10 µg/ml Proteinase K solution, post-fixed in 4% paraformaldehyde, washed in glycine and PTW, treated with 1% hydroxylammonium chloride and prehybridized 6 8 h in hybridization buffer.
To eliminate contaminating genomic DNA, the RNA preparations were treated with RNase-free DNase I (Invitrogen, Carlsbad, CA) and reverse-transcribed using Superscript II reverse-transcriptase and oligo dT 12 18 as primer (Invitrogen).
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After quantification of the concentration by spectrophotometry and confirmation by electrophoresis, 1 μg of the crude RNA preparations was treated with one unit of RNase-free DNase I (Promega).
To remove DNA, 10 μg preparations was treated with DNase (Turbo DNA-free kit, Ambion, Austin, TX) at 37°C for 30 min according to the manufacturer's instructions of Turbo DNA-free kit.
Nuclei from 1/5 of each preparation were treated with four ul of RNAse A, 10 ug/ul, (Qiagen) and used for Micrococcal Nuclease (Takara) digestion for 6 minutes (final concentration 0.2 U/ul) in digestion buffer (16 mM Tris-Cl, pH 7.6, 50 mM NaCl, 2.5 mM CaCl2, 0.01 mM PMSF and EDTA-free protease inhibitor cocktail (Roche) and stopped with 10 mM EDTA.
Mice used for the cell preparation were treated according to the guidelines of the IACUC Institutional Animal Care and Use Committeee) of the Medical College of Georgia to minimize pain or discomfort.
Each RNA preparation was treated with DNase I according to the manufacturer's instructions.
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