The authors used gBlocks® Gene Fragments to generate a standard curve for their qPCR analysis.
Target-capture using xGen Lockdown Probes was combined with throughput RNA sequencing to provide high resolution detection of known gene fusions. The targeted gene fusions were known to be associated with several childhood sarcomas.
xGen Lockdown Probes were used to target an entire coding region, exon-intron boundaries, and segments of DNA containing known pathogenic variants in BRCA1 and BRCA2 genes.
Changes in short RNA abundance were tested for their possible influence on mRNA levels of 10 relevant genes. RT-qPCR expression analysis was performed on the 10 genes that displayed clear changes in short RNA read numbers in both sense and antisense orientation and their neighboring genes. cDNA was amplified using PrimeTime qPCR Assays (primers and 5' hydrolysis probes). Expression values represented the ΔCt values compared to β-actin.
Hammond SM, McClorey G, Nordin JZ, Godfrey C, Stenler S, Lennox KA, Smith CE, Jacobi AM, Varela MA, Lee Y, Behlke MA, Wood MJ, Andaloussi SE.
Correlating in vitro splice switching activity with systemic in vivo delivery using novel ZEN-modified oligonucleotides
Mol Ther Nucl Acids,
The expression of 9 genes [Actn2, Actn3, Casq1, Drd2, Lepr, Mc4r, Mstn, Papss2, and Glut4 (a.k.a. Slc2a4)] with putative roles in the regulation of voluntary physical activity was evaluated via RT-qPCR of skeletal muscle and brain RNA from inherently high- and low-active mice. cDNA was amplified using PrimeTime Predesigned qPCR Assays, which included ZEN Double-Quenched Probes, with all reactions run in duplicate. Expression was normalized to an endogenous control (18S ribosomal RNA (IDT assay: RN18S) using methods described by Pfaffl.
Immunoprecipitated DNA was analyzed by real-time PCR using IDT PrimeTime qPCR Assays containing a ZEN Double-Quenched Probes and primers.
gBlocks Gene Fragments were used to generate mutant autonomously replicating sequences, or ARSs, associated with replication origins in yeast chromosomal DNA.
A gBlocks Gene Fragment was used to create an sgRNA expression vector for use with the CRISPR/Cas9 system.
gBlocks Gene Fragments were used to create sgRNA expression plasmids.
An RT-qPCR assay for HCV quantification was performed with probe-based assays using IDT primers and ZEN double-quenched probes.The assay amplified the 5′ UTR of the HCV genome and provided reduced background and increased signal.
The authors explain how next generation sequencing has advanced mitochondrial genetics research. They note how IDT’s xGen Lockdown Probes can be used to accomplish solution phase capture of mtDNA.
5 gBlocks Gene Fragments were used to assemble the ~2 kb coding sequence for Micalcl (NM_027587).
Sarvestani ST, Tate MD, Moffat, JM, Jacobi AM, Behlke, MA, Miller AR, Beckham SA, McCoy CE, Chen W, Mintern JD, O’Keeffe M, John M, Williams BR, Gantier MP.
Inosine-mediated modulation of RNA sensing by Toll-like receptor 7 (TLR7) and TLR8
α6A and α6B were amplified using IDT PrimeTime qPCR Assays. The assays were composed of primers and double-quenched hydrolysis probes containing the 5′ fluorophore FAM, and ZEN and IABkFQ quenchers. Relative mRNA levels were established by normalization to a pool of cDNA and calculated according to the Pfaffl mathematical model.
Dudek H, Wong DH, Arvan R, Shah A, Wortham K, Ying B, Diwanji R, Zhou W, Holmes B, Yang H, Cyr WA, Zhou Y, Shah A, Farkiwala R, Lee M, Li Y, Rettig GR, Collingwood MA, Basu SK, Behlke MA, Brown BD.
Knockdown of β-catenin with Dicer-substrate siRNAs reduces liver tumor burden in vivo