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For nuclear extracts and dephosphorylated proteins rehydratation buffer were added by buffer exchange using Protein Desalting Spin Columns (Pierce) according to the manufacture's method.
For the standard protocol, laboratory personnel were only involved with the initial transfer of 1000 μL of each specimen to individual sample cartridges placed inside the instrument after which proteinase K and buffers, including 450 μL of lysis buffer, were added by the instrument in a sequential and automated fashion.
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Reactions were started 15 sec after the buffer was added by adding 5 μL 60 mM ATP, and reactions were capped, vortexed, and placed in a 37°C water bath.
1.25 µl 10 mM dNTPs and 2.5 µl 5x buffer were added followed by 0.5 µl (5 U) AMV (Promega).
In the competitor dsDNA wells, 80 μL transcription factor assay buffer were added followed by 10 μL PPAR competitor dsDNA.
Subsequently, 100 μl of anti-biotin microbeads and 150 μl of MACS buffer were added followed by incubation at 4°C for 15 minutes.
In the positive control wells, 90 μL of transcription factor assay buffer were added followed by 90 μL of positive control.
To the pellet, the 150-μl second-strand syntheis reaction and 150 2× BW buffer were added, mixed by gentle vortexing and incubated on gentle rotation using a RotaMix (Elmi) at room temperature (≈22°C) for 15 minutes.
After the synthesis of QDs, 50 μL of 2 mg/mL QDs and 400 μL of 2 mg/mL sheep-anti-human secondary antibodies were mixed, and then 300 μL of 1-ethyl-3- 3-dimethylaminopropyl -carbodiimide EDC (44 mM in borate buffer) were added and blended by vortex.
Once dissolved, 180 µl of SDS sample loading buffer were added and the samples neutralized by addition of 7.5 µl of 5 m NaOH.
After incubation, 400 μl of binding buffer were added and cells were analysed by flow cytometry with FACScalibur (Becton Dickinson) and data were processed using FlowJo software, determining the percentage of apoptotic cells.
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