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Briefly, equal volumes of 20× Taqman gene expression assay (see below for primers) were combined in a pooled assay mix.
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A set of 384 SNPs was selected to develop an Illumina Golden Gate® oligonucleotide pooled assay.
cDNAs (2 μl) were preamplified in a 20-μl reaction for 10 cycles, using TaqMan PreAmp Master Mix and pooled assays.
Since the response from a well may be due to any or many of the peptides in the pool, pooled assays usually need to be followed by confirmatory assays of a number of individual peptides.
Each cDNA was preamplified on two sets of 218 pooled assays.
Of the 6738 loci included in the Illumina oligo pooled assays, 5815 (86.3%) were successfully typed and 4690 of the 5815 (80.7%) were assigned to the RH map.
A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle-derived SNP (Single Nucleotide Polymorphism), originated from Oligo pooled assays (OPA) synthesized and assembled by Illumina Inc. (San Diego, CA).
Four quality assurance specimens were included in each assay: i) a pooled serum sample from women of a similar age from the study participants, ii) one randomly drawn case sample, iii) one randomly drawn control sample, and iv) a pooled sample of the selected case and control samples.
Here we report excellent coverage of amplification, confirmed on a whole genome level using an oligonucleotide pool assay.
To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA) for interrogation of 1524 loci, of which 1153 loci had known genetic map positions.
Thermocycling was as follows: 50°C for 2 min and 95°C for 10 min followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. Genetic marker analysis was done using an Illumina GoldenGate BeadArray (Illumina, San Diego, USA) with an Oligo Pool Assay (OPA) for interrogation of 1524 barley markers [ 36].
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