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For each infection experiment, total RNA samples were obtained from infected and mock-infected cells at 8 hours post-infection and checked for quantity and quality (Nanodrop, Agilent).
Total RNA was then extracted from the aqueous phase with RNeasy kit (Invitrogen) according to manufacturer's instructions and checked for quantity and integrity using an Agilent 2100 bioanalyzer.
Amplified RNAs were checked for quantity and quality by spectrophotometry and Bioanalyzer.
Amplified RNAs were checked for quantity and quality by spectrophotometry and agarose gel electrophoresis.
The purified DNA was checked for quantity and purity using a NanoQuant Tecan M200 (Tecan, Durham, NC, USA).
RNA pellets were washed with 70% ethanol, resuspended in TE, and checked for quantity and integrity as described above.
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RNA was extracted and checked for quality and quantity as described above.
Each RNA sample was linearly amplified, following the Eberwine procedure [20] using the Two-cycle Amplification Method (Affymetrix), and again checked for quality and quantity.
Protein contents of the extracts were measured in triplicate by Bradford method and checked for quality and quantity by comparing pattern intensities in SDS-PAGE.
Extracted DNA was checked for quality and quantity by Nanodrop and gel analyses.
The product is re-amplified and checked for quality and quantity.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com