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An RNeasy Mini Kit (Qiagen Valencia, CA) was used to purify the mRNA, which was then treated with DNase I (Epicentre Biotechnologies, Madison, WI) in NEBuffer 2 (New England BioLabs, Ipswich, MA) to remove genomic DNA and reverse-transcribed with SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen, Carlsbad, CA).
20 µg of amplified DNA of each sample was fragmented in 1×One-Phor-All Buffer plus (GE Healthcare) using 1∶50 dilution of DNAse I (Epicentre) for 9 minutes at 37°C followed by heat inactivation at 100°C for 10 minutes and snap cooling on ice for 2 minutes.
12S/16S mtDNA was amplified using the following PCR cocktail (50 µL final volume): 25 µL FailSafe PCR 2× Premix I (Epicentre, Madison, WI); 14.5 µL ultra pure water (Water Optima, Fisher Scientific, Hampton, NH); 5 µL of each 2.5 pM/µL primer; 0.5 µL Taq DAN polymerase (Invitrogen, Carlsbad, CA); and 1 µL genomic DNA.
Cy3-labeled cDNAs were fragmented to the 50 to 300 bp range with DNase I (Epicentre).
The DNA template was digested with 1 U/μl RNase-free DNase I (Epicentre).
RNA pellets were resuspended in TE buffer and treated with DNase I (Epicentre) to remove contaminating genomic DNA.
Similar(49)
Reactions were prepared similarly to EMSA and after 40 min incubation, the mixtures were treated with a dilute DNase I solution (Epicentre) for 5 minutes, as described previously [30].
Multiplex PCR products amplified by HotStarTaq (Qiagen) were purified with shrimp alkaline phosphatase (SAP) (Promega, Madison, USA) and Exonuclease I (ExoI) (Epicentre, Madison, USA).
DNA fragments remaining in the total RNA isolate were digested by DNase I (Baseline-ZERO, Epicentre).
Sequencing reactions contained 4 pmol of each IRD (infrared-dye -labelled M13 prinfrared-dye -labelledm Excel™infrared-dye -labelledcentre Technologies) and buffer prescribed by the M13ufacturer.
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