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Recently, we successfully explored the feasibility of a protocol in which T-array analysis is preceded by simultaneous amplification of all Vβ families in one PCR reaction using anchored PCR as described earlier [19], [20] (data not shown).
Nos2 PCR genotyping was performed according to The Jackson Laboratory standard procedures by simultaneous amplification of the WT (Nos2+) and knockout (Nos2-) alleles using three primers: oIMR1216, 5'-ACATGCAGAATGAGTACCGG-3'; oIMR1217, 5'-TCAACATCTCCTGGTGGAAC-3'; and oIMR1218, 5'-AATATGCGAAGTGGACCTCG-3'.
Detection of influenza A and B viruses in clinical samples was accomplished by simultaneous amplification of specific sequences located within the NS-2 gene of either virus using the primer sets (Table 1) designed originally by Claas et al. [ 14].
To overcome these technical limitations, we used a multiplexed MSRE enrichment strategy allowing for the reduction of unmethylated background DNA followed by simultaneous amplification of 96 targets (Supplemental Fig. S11).
Cybb PCR genotyping was performed according to The Jackson Laboratory standard procedures by simultaneous amplification of the WT (Cybb+) and knockout (Cybb-) alleles using three primers: oIMR0517, 5'-AAGAGAAACTCCTCTGCTGTGAA-3'; oIMR0518, 5'-CGCACTGGAACCCCTGAGAAAGG-3'; and oIMR0519, 5'-GTTCTAATTCCATCAGAAGCTTATCG-3'.
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The linear regression line for ng of DNA was determined from relative fluorescent units (RFU) at a threshold fluorescence value (Ct) to quantify gene targets from cell extracts by comparing the RFU at the Ct to the standard curve, normalized by the simultaneous amplification of RpL13a, a housekeeping gene.
Multiplex-PCR assays were performed by the simultaneous amplification of the see, seg, seh, sei, selj, selm, seln, selo, selk, selq, selr, and selu sequences using the primer sets listed in Table 1.
Complete viral genomes were amplified by multisegment reverse-transcription PCR (M-RTPCR), a method that allows simultaneous amplification of all viral segments by using a pair of universal primers targeted against highly conserved flanking regions, as previously described [ 11].
A set of 11 multiplex panels for the simultaneous amplification of the 30 most informative markers (ranked by their Polymorphism Information Content) is made available.
However, the use of microarray-based DNA methylation analysis has been limited by the low throughput of sample preparation due to the difficulty in simultaneous amplification of multiple targets.
For genotyping, we first performed multiplex PCR, a variant of PCR that enables simultaneous amplification of many targets of interest in one reaction by using more than one pair of primers [ 16].
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