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Regions of the model that do not align to the template are treated as loops, which must be predicted "ab initio".
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After that, the AAO template was treated again in a 5 wt% phosphoric acid solution at 35°C for 20 min to remove the AAO barrier layer.
To remove the barrier layer, AAO template was treated with 5 wt% phosphoric acid solutions at 35°C for ca. 20 min. The SEM image of the obtained structure is given in Fig. 3b, which shows the surface of the AAO template with opened AAO barrier layer.
RNA template was treated with DNase to avoid the contamination by genomic DNA in the reverse transcription-PCR of this intronless gene.
All these methods were based on PCR and the template was treated with sodium bisulphite.
The immobilised template was treated for 5 s each with 70% ethanol, denaturation buffer, and then washing buffer, and transferred to a PSQ 96 plate (Biotage, Uppsala, Sweden).
Preparation of the 5′-radiolabeled RNA template was performed as follows: The gel-cleaned RNA template was treated with shrimp alkaline phosphatase (SAP, Fermentas) at 37 °C for 60 min and then incubated at 65 °C for 25 min to inactivate the enzyme.
Afterwards, the radio-frequency power (50 W, 13.56 MHz) was applied, and alumina templates were treated by the discharge plasma for 5 min.
Reverse transcription reactions were performed using the SuperScript First-Strand Synthesis System (Invitrogen, CA), and the RNA templates were treated with DNase to avoid genomic DNA contamination.
Approximately 500 ng of SMRTbell templates were treated with the Tet1 enzyme at 37°C for 60 minutes followed by proteinase K treatment at 50°C for 60 minutes.
The sample containing all reagents except the template DNA was treated as the negative control.
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