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The first PCR in the 5' RACE (3' RACE) was performed using the 5' RACE (3' RACE) outer primer supplied in the kit (Ambion) and primers specific for the respective subunit (Table S2).
A forward primer (5'-CAGAACTCATGGGGCAGCGGTGATTTGT-3'; residues 535-544 of zebrafish lamin A) and a forward nested primer (5'-GCGGTGATTTGTTCCAGACCACCCTCAT-3'; residues 540 549 of zebrafish lamin A) were used to amplify the 3'-end portion of the zebrafish cDNA by PCR in conjunction with the adapter primer supplied with the kit (Invitrogen).
First, the method of Zhang et al. [31] was used with slight modifications: the 3'RACE library described above was amplified with the primers AUAP (adapter primer supplied with the kit) and dinoSL [31] to enrich for full transcripts (PCR program: 94°C - 60 s; 30× 94°C - 30 s, 68°C - 5 min); 68°C - 10 min; 8°C hold; PCR chemistry see below).
For the detection of DRAM1 siRNA knock down, we used primer supplied by Qiagen (Hs_DRAM1_1_SG).
Thirty more cycles of PCR were further carried out using the inner 5' RNA adaptor primer supplied in the kit and inner 3' gene-specific primer.
The purified RNA was reverse transcribed using the RevertAid H Minus First Strand cDNA Synthesis Kit (Fermentas) with the oligo dT 18 primer supplied by the manufacturer.
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The Oligo dT primer supplies a priming site for the GeneRacerTM 3' PCR primers.
3' RACE PCR reactions were carried out using gene specific primers and anchor primers supplied with the kit.
For this the cDNA for each selected miRNA was synthesized by using the miRNA specific primers supplied by the manufacturer (Applied Biosystems).
To get a longer cDNA sequence, we performed 3'-RACE and 5'-RACE using nested gene-specific primers for SeEcR (Table 2) and anchor primers supplied in a SMART RACE cDNA Amplification Kit (Clontech).
To get a longer cDNA sequence, we performed 3'-RACE using gene specific primers for sid-1 and anchor primers supplied in a SMART RACE cDNA Amplification Kit (Clontech).
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