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RNA was converted to cDNA using a universal cDNA synthesis kit (Exiqon, Vedbaek, Denmark).
Briefly, 25 ng of purified total RNA was used to generate cDNA, using a Universal cDNA Synthesis Kit according to the manufacturer's protocol (number 203300; Exiqon, Denmark).
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In brief, the RNA were tailed with a poly(A) sequence at their 3'end and then reverse transcribed into cDNA using a universal poly(T) primer with a 3'end degenerate anchor and a 5'end universal tag.
In brief, the RNA was tailed with a poly (A) sequence at their 3′end and then reverse transcribed into cDNA using a universal poly (T) primer with a 3′end degenerate anchor and a 5′end universal tag.
To characterize further the diversity of the finTRIMs, we performed a 3'RACE PCR on VHSV-induced leukocyte cDNA using a universal primer specific for trout finTRIM localized in the highly conserved region in the vicinity of the start codon.
In rainbow trout, the 3'-RACE PCR was performed from VHSV-induced leukocyte cDNA using a universal primer specific for trout finTRIM localized in the highly conserved region around the start codon.
Real-time RT-PCR was performed with 40 ng cDNA, using a universal PCR master mix reagent kit (Applied Biosystems) and the following cycling parameters: Uracil-N-glycosylase (UNG) activation at 50°C for 2 min, AmpliTaq activation at 95°C for 10 min, denaturation at 95°C for 15 sec and annealing/extension at 60°C for 1 min (repeat 40 times) on ABI7000.
A custom cDNA microarray using a universal DNA reference design was used to examine trends of altered gene expression across sewage concentrations, across timepoints, and at the end of the recovery period.
Full-length CYP cDNAs were cloned using a universal cloning method based on the site-specific recombination system of bacteriophage lambda (Invitrogen Corp .. Based on the 5'- and 3'-end sequences, one primer set for cloning of full-length CYP cDNA was designed to the 5'-UTR region for the forward primer and to the 3'-UTR region for the reverse primer.
To detect the mature miRNA strand of either miR or miR*, the first-strand cDNA synthesis was carried out using a universal reverse primer and the Universal RT miRNA PCR System (Exiqon).
RNA quality was assessed with an Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, USA) and RNA was converted to cDNA using the Universal cDNA synthesis kit at 60 min at 42°C and 5 min at 95°C, and cooled to 4°C.
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