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Unincorporated dye was removed using a QIAquick Nucleotide Removal Kit (QIAGEN) as specified in the manufacturer's protocol.
1 μg of Col-0 10-d-old shoot DNA or synthetic control DNA was incubated with 50 units of TaqαI and 100 μg of RNase A at 60 ° for 1 hr; 2.5 units of shrimp alkaline phosphatase were added and samples were incubated at 37 ° for 30 min. DNA fragments were isolated using a QIAquick Nucleotide Removal kit (Qiagen).
The DNA was cleaned up with a QiaQUICK PCR purification kit (Qiagen), eluted in 50 µL of elution buffer (EB) and then digested overnight with 20 U of Csp6I (Fermentas) in buffer B. DNA was purified using a QiaQUICK Nucleotide Removal Kit (Qiagen) and ligated with Quick ligase in the presence of 10-fold excess of adaptor P1-BtnAM and P1-BtnB.
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Unincorporated fluorescent nucleotides were removed using a Qiaquick PCR purification kit (Qiagen).
The unincorporated nucleotides were removed using a QIAquick PCR purification column (Qiagen) and the labeled probe is eluted with 2 × 25 ul washes.
Finally, the DNA was purified using a QiaQuick PCR purification kit (Qiagen).
The cDNA fragments were purified using a QIAquick PCR extraction kit.
Samples were purified using a QIAquick gel extraction kit.
Products of the secondary PCR reaction were purified using a QIAquick purification column (QIAGEN).
Resulting PCR products were purified using a QIAquick Spin PCR purification kit (Qiagen).
The PCR products were gel-purified using a QIAquick gel extraction kit (QIAgen, Hilden, Germany).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com