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Briefly, one microgram of genomic DNA was first mixed with 5 µl of M-Dilution Buffer and incubated at 37°C for 15 minutes and then mixed with 100 µl of CT Conversion Reagent prepared as instructed in the protocol.
After labeling tumor DNA and reference DNA samples were pooled, cleaned and hybridization cocktails were prepared as instructed in the protocol.
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Digested tumor and reference DNAs were labeled with Cy5-dUTP and Cy3-dUTP, respectively (Genomic DNA labeling Kit Plus, Agilent Technologies, Palo Alto, CA), pooled and hybridized as instructed in the manufacturers protocol.
PSVue 794 binding was measured using the LI-COR Odyssey Image System for NIR emission, as instructed in the application protocol manual [ 36].
The supernatant was reacted with luciferase reagent as instructed in the manufacturer's protocol.
For each sample, we constructed two independent first-strand cDNA libraries using up to 5 μg of total RNA, Oligo-dT18 primers and the Revert AidTM H Minus First Strand cDNA Synthesis Kit (Fermentas/Thermo Scientific, Waltham, MA, USA) as instructed in the manufacturer's protocol.
This mixture was added to a DNA spin column, and DNA recovery protocols were followed as instructed in the QIAamp DNA Mini Kit (QIAGEN, CA, USA) starting at step 5 of the Tissue Protocol.
This mixture was added to a DNA spin column, and DNA recovery protocols were followed as instructed in the QIAamp DNA Mini Kit (Qiagen, Valencia, CA) starting at step 5 of the Tissue Protocol.
This mixture was added to a DNA spin column, and DNA recovery protocols were followed as instructed in the QIAamp DNA Mini Kit (Qiagen) starting at step 5 of the Tissue Protocol.
was used as instructed in the manual.
Detected bands were quantified using Image J v1.43 as instructed in the software manual.
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