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This set of 369 SNPs was submitted for Illumina GoldenGate oligo assay pool (OPA) design, where duplicate SNPs and those that will potentially adversely affect the performance of the assay were removed.
T-PreAmp of this primer/gene assay pool was carried for 14 cycles on a PTC-100 Programmable Thermal Controller (MJ Research, Watertown, Massachusetts, USA) with the following program: denaturation at 95°C for 10 min and 14 cycles of amplification (15 sec at 95°C, 4 min at 60°C).
It is advantageous to use a large assay pool in preamplification.
Typing was carried out in five multiplex reactions which included all 6738 loci in the final assay pool.
Of the 10 631 candidate SNPs submitted for scoring, 6738 were included as part of the final assay pool.
miRNA expression profiles of native and day 7 osteo-differentiated USSC were analyzed using the RT-PCR-based TaqMan Assay (Pool A) covering 377 miRNAs [ 43].
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Four assay pools (30, 28, 28, and 24 SNPs) were created for multiplexing.
We applied parallel mutant phenotyping by barcode sequencing (Bar-seq) to assay pooled haploid deletion mutants as they aged together during long-term quiescence.
In brief, specific assay pools were designed using AssayDesignersoftware in MassARRAY Typerpackage software (v4.0) with filters for proximal single nucleotide polymorphisms (SNPs) and assessment of the specificity of PCR amplification and the subsequent primer extension reaction.
The motivation for assaying pooled samples of DNA rather than individual samples is to reduce costs.
However, for a fixed number of assays, pooled samples produced far better results than one random individual assayed from each pool.
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