PrimeTime® qPCR Assay Citations

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  1. HCV infection selectively impairs Type I but not Type III IFN signaling
    Chandra PK, Bao L, et al
    Am J Pathol, 184(1):214-229 (2014)
    An RT-qPCR assay for HCV quantification was performed with probe-based assays using IDT Primers and ZEN double-quenched probes. Note that these IDT reagents were compatible and performed well with Bio-Rad iQ Supermix master mix on a CFX96 real-time PCR system with CFX Manager software version 1.0. The assay amplified the 5′ UTR of the HCV genome using:
    sense primer 5′-TCTTCACGCAGAAAGCGTCTA-3′ (60–80; HCV/S)
    antisense primer 5′-CGGTTCCGCAGACCACTATG-3′ (157–138; HCV/AS).
    The probe 5′-/56-FAM/TGAGTGTCG/ZEN/TGCAGCCTCCAGGA/3IBκFQ/-3′ (Integrated DNA Technologies, Coralville, IA), labeled at the 5′ ends with a 6-carboxyfluorescein (FAM) fluorophore reporter molecule and ZEN-Iowa Black FQ (IBFQ) double quenchers, was used to reduce the background and increase signal.
    ZEN, probe-based assays, microbial
  2. A disulphide-linked heterodimer of TWIK-1 and TREK-1 mediates passive conductance in astrocytes
    Hwang EM, Kim E, et al
    Nature Commun, 5: (2014)
    PrimeTime qPCR Assays (primers and probes) for TRAAK, TASK-1, TASK-2, TALK-1, TRESK-2, and GAPDH were used in this study. Experiments were repeated a minimum of three times. The 2ΔΔCt method was used to calculate fold changes in gene expression.
    probe-based assays, mammalian
  3. Noninvasive imaging of Staphylococcus aureus infections with a nuclease-activated probe
    Hernandez FJ, Huang L, et al
    Nature Med, doi:10.1038/nm.3460: (2014)
    IDT synthesized and purified all oligonucleotide probes. The FAM-labeled probes were synthesized using standard solid-phase phosphoramidite chemistry, followed by HPLC purification.\Cy5.5-labeled probes werew initially synthesized with ZEN and Iowa Black quenchers or inverted dT on the 3′ ends and amine on the 5′ ends, using the standard solid-phase phosphoramidite chemistry. These molecules were purified with HPLC. The purified sequences were then reacted with Cy5.5 NHS ester (GE Healthcare) to chemically conjugate the Cy5.5 label to the sequences, followed by another round of HPLC  purification. Probe identities were confirmed using electron spray ionization mass spectrometry (ESI-MS).
    ZEN, microbial
  4. Arylbenzofuran isolated from Dalbergia odorifera suppresses lipopolysaccharide-induced mouse BV2 microglial cell activation, which protects mouse hippocampal HT22 cells death from neuroinflammation-mediated toxicity
    Lee D-S, Jeong G-S
    Euro J Pharmacol, doi: 10.1016/j.ejphar.2013.12.041: (2014)
    Real-time PCR was performed using SYBR Green intercalating dye and primers designed using the IDT PrimerQuest Primer Design Tool and synthesized by IDT. The primer sequences were: HO-1, forward 5'-CTCTTGGCTGGCTTCCTT-3', reverse 5'-GGCTCCTTCCTCCTTTCC-3', and glyceraldehydes-3-phosphate dehydrogenase (GAPDH), forward 5'-ACTTTGGTATCGTGGAAGGACT-3', reverse 5'-GTAGAGGCAGGGATGATGTTCT-3. Relative gene expression (target gene expression normalized to the expression of the endogenous control gene) was calculated using the comparative Ct method (2−ΔΔCt).
    plants, intercalating dye assays, PrimerQuest Custom Design Tool
  5. Integrin α6A splice variant regulates proliferation and the Wnt/β-catenin pathway in human colorectal cancer cells
    Grouix J-F, Giroux V, et al
    Carcinogen, doi: 10.1093/carcin/bgu006: (2014)
    α6A and α6B were amplified using IDT PrimeTime qPCR Assays 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.
    probe-based assays, mammalian, ZEN
  6. Contribution of natural antisense transcription to an endogenous siRNA signature in human cells
    Werner A, Cockell S, et al
    BMC Genomics, 15(19):doi:10.1186/1471-2164-15-19 (2014)
    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.
    probe-based assays
  7. Differential gene expression in high- and low-active inbred mice
    Dawes M, Moore-Harrison T, et al
    BioMed Res Internat, doi: 10.1155/2014/361048: (2014)
    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.
    PrimeTime qPCR Assay Selection Tool, mammalian, ZEN
  8. Prevalence and abundance of Staphylococcus aureus in the middle meatus of patients with chronic rhinosinusitis, nasal polyps, and asthma
    Ramakrishnan VR, Feazel LM, et. al
    Int Forum Allergy Rhinol, 3(4):267–271 (2013)
    Use of IDT PrimeTime qPCR Assays to determine the proportion of Staphylococcus aureus to total bacteria populations in individuals with chronic rhinosinusitis.
    probe-based assays, microbial
  9. Gain-of-function mutant p53 downregulates miR-223 contributing to chemoresistance of cultured tumor cells
    Masciarelli S, Fontemaggi G et al
    Oncogene, doi: 10.1038/onc.2013.106. (ePub ahead of print): (2013)
    Immunoprecipitated DNA was analyzed by real-time PCR using IDT PrimeTime qPCR Assays containing a ZEN Double-Quenched Probes and primers.
    ZEN, probe-based assays, mammalian
  10. Jun Is required in Isl1-expressing progenitor cells for cardiovascular development
    Zhang T, Liu J, et al
    PLOS One, doi:10.1371/journal.pone.0057032.s002: (2013)
    The scientists used IDT PrimeTime qPCR Assays for mouse genotyping.
    genotyping, probe-based assays, mammalian
  11. Brain region- and age-dependent dysregulation of p62 and NBR1 in a mouse model of Huntington's disease
    Rue L. Lopez-Soop G, et al
    Neurobio Disease, 52:219-228 (2013)
    A PrimeTime Mini qPCR Assay was used for detection of 18S rRNA (PrimeTime Std qPCR Assay) and NBR1 (Mm.PT.45.6651111) in tissue from the striatum and cortex of wild type and R6/1 mice.
    probe-based assays, mammalian
  12. Peripheral administration of d-cycloserine rescues memory consolidation following bacterial endotoxin exposure
    Kranjac D, Koster KM et al
    Behav Brain Res, 243:38-43 (2013)
    PrimeTime qPCR Primers and the intercalation dye, BRYT Green dye, were used to determine the initial amount of RNA present in samples and to normalize this amount using a B-actin endogenous control assay. The PrimeTime Primers utilized were designed to span the intron splice junction (thus avoiding amplification of genomic DNA) between IL-1β exon locations 2–4, BDNF exon locations 2–5, NR1 exon locations 2–3, NR2C exon locations 6–7, and β-actin exon locations 5–6. Gene expression levels were calculated from the qPCR data by normalizing the amplification rate of the target gene's expression against the amplification rate of β-actin, using the DART-PCR method, which does not assume a perfect amplification efficiency for all cycles.
    intercalating dye assays, mammalian
  13. Prolonged diet induced obesity has minimal effects towards brain pathology in mouse model of cerebral amyloid angiopathy: Implications for studying obesity–brain interactions in mice
    Zhang L, Dasuri K, et al
    Biochim Biophys Acta, 1832(9):1456-1462 (2013)
    PrimeTime Predesigned qPCR Assays that included 6-FAM/ZEN/IBFQ Double-Quenched Probes were used in conjunction with reverse transcription reactions for detection of TNF-α, IL-1β, IL-6 and GAPDH.
    probe-based assays, ZEN, mammalian
  14. Development of a Locked Nucleic Acid Real-Time Polymerase Chain Reaction Assay for the Detection of Pinus armandii in Mixed Species Pine Nut Samples Associated with Dysgeusia
    Handy S, Timme R, et al
    J Agric Food Chem, 61(5):1060-1066 (2013)
    The group designed a PrimeTime qPCR LNA Probe targeting a P. armandii SNP sequence.The probe was 24 bases long and contained 6 LNA bases in addition to the 5′ 6-FAM label and 3′ black hole quencher (3BHQ_1). A second PrimeTime qPCR LNA Probe was designed to serve as a blocker probe for species of trees related to the species of interest,  Pinus armandii. The probe was also 24 bases long with 6 LNA bases in addition to a 5′ HEX label and a 3′ BHQ.  These reporter dyes (HEX and FAM) can be spectrally resolved from each other because they emit at different wavelengths.
    LNA, probe-based assays, plants
  15. An in-house assay for BK polyomavirus quantification using the Abbott m2000 RealTime System
    Muldrew K, Lovett J
    J Med Microbio, PMID: 23924663, ePub ahead of print: (2013)
    IDT PrimeTime qPCR Primers and a ZEN Double-Quenched Probe were used throughout this work. In initial studies, the  ZEN Double-Quenched Probe was compared to a second identical TaqMan probe that did not contain the ZEN quencher. Serial low level dilutions demonstrated increased sensitivity of the probe containing the IDT ZEN quencher.
    probe-based assays, ZEN, microbial
  16. Prognostic value of EGFR mutation and ERCC1 in patients with non-small cell lung cancer undergoing platinum-based chemotherapy
    Yamashita F, Azuma K, et al
    PLoS One, 8(8):e71356 (2013)
    PNA (peptic nucleic acid-locked nucleic acid) clamp Primers and LNA (locked nucleic acid) mutant probes from IDT were used in a PNA-LNA PCR clamp assay for EGFR mutation analysis.
    LNA, probe-based assays, mammalian
  17. Expression of substance P, neurokinin-1 receptor and immune markers in the brains of individuals with HIV-associated neuropathology
    Spitsin S, Stevens K, Douglas S
    J Neurol Sci, doi: 10.1016/j.jns.2013.07.008. [Epub ahead of print]: (2013)
    The researchers use all IDT PrimeTime qPCR Primers and Probes for this study. In some cases PrimeTime qPCR Primers were used with the intercalation dye, SYBR Green Dye. In other cases PrimeTime qPCR Probes were used. The probe targeting TAC-1 (SP) included the ZEN Quencher to create a ZEN-IBFQ Double-Quenched Probe for TAC-1 (SP) detection.
    probe-based assays, ZEN, mammalian
  18. Complex seasonality observed amongst diverse phytoplankton viruses in the Bay of Quinte, an embayment of Lake Ontario
    Rozon RM, Short SM
    Freshwater Biol, DOI: 10.1111/fwb.12241: (2013)
    All newly designed qPCR probes in this study and the extant LO.16jul08.20 probe were 5′ labelled with FAM (6-carboxyfluorescein) and 3′ labelled with the IDT ZEN Quencher. Additional probes were 3′ labelled with IDT Iowa Black FQ.
    ZEN, probe-based assays, microbial
  19. Nicotinic acetylcholine receptor antagonists alter the function and expression of serine racemase in PC-12 and 1321N1 cells
    Singh NS, Paul RK, et al
    Cell Signal, doi: 10.1016/j.cellsig.2013.08.025: (2013)
    Quantitative RT-PCR reactions were performed to determine the expression of the different subunits of CHRN mRNA using the PrimeTime qPCR Assays (Primers and Probe sets)
    probe-based assays, mammalian
  20. microRNA-150 expression induces myeloid differentiation of human acute leukemia cells and normal hematopoietic progenitors
    Morris VA, Zhang A, et al
    PLOS One, 8(9):e75815. doi:10.1371/journal.pone.0075815 (2013)
    In these studies mRNA expression was analyzed using IDT PrimeTime qPCR Assays on duplicate samples with relative expression reported as ΔCt and ΔΔCt normalized to GUSB. 
    probe-based assays, mammalian
  21. Activated phenotype of circulating neutrophils in familial Mediterranean fever
    Manukyan G, Petrek M, et al
    Immunobiol, 218(6):892-898 (2013)
    Quantitative RT-PCR, using IDT PrimeTime qPCR Assays, was performed on samples from patients suffering from the autoinflammatory disorder, Familial Mediterranean fever (FMF), to ascertain the expression signature of 12 immune genes that encode inflammation-related molecules. Relative expression compared to results from healthy controls was calculated using the second derivative method; target gene expression was normalized to the expression of the RPL32 gene.
    probe-based assays, mammalian
  22. Geographic setting influences Great Lakes beach microbiological water quality
    Haack SK, Fogarty LR, et al
    Environ Sci & Technol, DOI: 10.1021/es402299a: (2013)
    The researchers used a double-quenched probe, labeled with the IDT internal ZEN and 3' Iowa Black Quenchers to detect a gull-associated marker from Catellicoccus marimammalium (Gull2). The authors note that the double-quenched probe was used to reduce background and increase qPCR signal.
    probe-based assays, ZEN, microbial
  23. Preclinical validation of Aurora kinases-targeting drugs in osteosarcoma
    Tavanti E, Sero V, et al
    British Journal of Cancer, doi: 10.1038/bjc.2013.643: (2013)
    An IDT PrimeTime Standard qPCR Assay ( Hs.PT.56. 39182776), using a 6-FAM/ZEN/IBFQ Double-Quenched Probe and TaqMan Universal PCR Master Mix (Applied Biosystems), was used to detect ABCB1-mRNA.
    probe-based assays, ZEN, mammalian
  24. The molecular basis of the specificity and cross-reactivity of the NeuN epitope of the neuron-specific splicing regulator, Rbfox3
    Maxeiner S, Glassmann A, et al
    Histochem Cell Biol, DOI 10.1007/s00418-013-1159-9: (2013)

    The primers and probes used in the PCR assays to determine the splicing pattern of exons 12 and 15 were designed using the RealTime PCR Assay Design Tool and PrimerQuest Custom Design Tool, both free online software tools available through the IDT website (www.idtdna.com) under the SciTools tab. In addition, IDT ZEN Double-Quenched Probes (FAM/ZEN/IBFQ) were used in these assays.

    probe-based assays, ZEN, RealTime PCR Assay Design Tool, PrimerQuest Custom Design Tool, mammalian
  25. Early growth response-1 (Egr-1) and nuclear factor of activated T cells (NFAT) cooperate to mediate CD40L expression in megakaryocytes and platelets
    Crist SA, Elzey BD, et al
    J Biol Chem, doi:10.1074/jbc.M113.511881: (2013)
    Primers and probes corresponding to the proximal NFAT/EBS (PNFAT) and the distal
    NFAT sites were synthesized by IDT. FAM/ZEN/Iowa Black Dual-Quenched Probes were used with the ZEN Quencher serving as a second, internal quencher.

    ZEN, probe-based assays, mammalian
  26. Renal angiotensin II type 1 receptor expression and associated hypertension in rats with minimal SHR nuclear genome
    Collett JA, Hart AK, et al
    Physiol Reports, DOI: 10.1002/phy2.104: (2013)
    IDT ZEN Double-Quenched Probes were included in assays developed for qPCR experiments. For GAPDH, their reference gene, the researchers used an IDT PrimeTime Predesigned qPCR Assay
    ZEN, probe-based assays, PrimeTime qPCR Assay Selection Tool, mammalian
  27. A novel Zap70 mutation with reduced protein stability demonstrates the rate‐limiting threshold for Zap70 in T cell receptor signalling
    Cauwe B, Tian L, et al
    Immunol, DOI: 10.1111/imm.12199: (2013)
    PrimeTime Predesigned qPCR Assays for Zap70 (Mm.PT.56a.12463755) and &beta-actin (Mm.PT.56a.33540333) were purchased from IDT and used for qPCR experiments. 
    Relative gene expression was determined by the 2ΔΔct method and normalized to the average of wild type CD4+ T cells
    probe-based assays, PrimeTime qPCR Assay Selection Tool, mammalian
  28. Chondroitin sulphate N-acetylgalactosaminyl-transferase-1 inhibits recovery from neural injury
    Takeuchi K, Yoshioka N, et al
    Nature Commnunications, 4(2740): (2013)
    27 different IDT PrimeTime qPCR Assays containing FAM and ZEN/IABkFQ Double-Quenched Probes were use for real-time RT-PCR in conjunction with the iScript one-step RT-PCR kit (Bio-Rad), the SsoFast Probes supermix (Bio-Rad) to detect gene expression after  siRNA knockdown.
    probe-based assays, ZEN
  29. Maintained expression of genes associated with metabolism in the ventromedial hypothalamic nucleus despite development of leptin resistance during pregnancy in the rat
    Phillipps HR, Laydyman SR, Grattan DR
    Physiol Reports, 1(6):DOI: 10.1002/phy2.162 (2013)
    qPCR probe-based assays sets were used for identification of mRNA transcripts in laser capture microdissected VMN and arcuate nucleus samples in diestrous rats and day 14 pregnant rats. Oligonucleotide primer and probe sequences specific for Bdnf, Glucokinase and Pacap were designed using PrimerQuestSM software (IDT). β-actin was used as a reference gene and all probes (IDT) contained a 5′ 6-FAM reporter dye and both internal ZEN™ and 3′ Iowa black FQ quenchers for increased sensitivity
    ZEN, probe-based assays, PrimerQuest Custom Design Tool, mammalian
  30. Fast, reliable and low cost user-developed protocol for detection, quantification and genotyping of hepatitis C virus
    Davialieva K, Kiprijanovska S, Plaseska-Karanfilska D
    J Virol Meth, 196:104-112 (2013)
    Standard desalted IDT Primers and ZEN Double-Quenched Probes were used for HCV detection and genotyping. The primers and probe used in this study were designed based on 45 HCV sequences (obtained from GenBank) correspond to genotypes 1a, 1b, 2a, 2b, 2c, 3a, 3b and 4 according to the HCV genotype nomenclature.The developed assays for HCV detection and genotyping were set up to detect and discriminate four HCV genotypes.
    genotyping, ZEN, probe-based assays, microbial
  31. Development and application of a multiplex qPCR technique to detect multiple microcystin-producing cyanobacterial genera in a Canadian freshwater lake
    Ngwa FF, Madramootoo CA, Jabaji S
    J Applied Phycol, DOI 10.1007/s10811-013-0199-9: (2013)
    3 probe fluorescent chemistries were used in single tube multiplex qPCR assays to differentially detect 3 cyanobacterial genera. The Anabaena mcyE probe was a ZEN Double-Quenched Probe (IDT) containing a 5' FAM fluorescent reporter dye, an internal ZEN moiety, and Iowa Black® FQ (IABkFQ) Quenchers (IDT) at the 3' end. It was used along with assays containing HEX labeled probes to Microcystis and Planktothrix mcyE.
    The optimized multiplex qPCR reaction mixture (25 μL) contained 12.5 μof 2× Brilliant Multiplex QPCR Master Mix (Agilent Technologies), 30 nM ROX reference dye, 400 ng μL-1, BSA, and optimized concentrations of the Anabaena, Mcirocyctis,and Planktothrix specfiic primers and probes. Concentrations of primers and probes were initially optimized
    in singleplex qPCR reactions.
    ZEN, probe-based assays, multiplex, microbial
  32. Enhanced reliability and accuracy for field deployable bioforensic detection and discrimination of Xylella fastidiosa subsp. pauca, causal agent of citrus variegated chlorosis using Razor Ex technology and TaqMan quantitative PCR
    Ouyang P, Arif M, et al
    PLOS One, DOI: 10.1371/journal.pone.0081647: (2013)
    This report describes use of Razor Ex in a field-deployable rapid and reliable bioforensic method for early, accurate, and sensitive detection of a bacterial phytopathogen based on multigene targets.of Xfp (a xylem-limited bacterium that causes citrus variegated chlorosis [CVC]) in plant tissues. Two sets of specific PCR primers and probes, targeting Xfp genes for fimbrillin and the periplasmic iron-binding protein were designed. Also used was a third pair of primers targeting the conserved cobalamin synthesis protein gene for detecting all possible X. fastidiosa (Xf) strains. All three primer sets detected as little as 1 fg of plasmid DNA carrying X. fastidiosa target sequences and genomic DNA of Xfp at as little as 1-10 fg. qPCR assays were performed with primers and ZEN Double-Quenched Probes (5’ 6-carboxyfluorescein/ZENTM/3’ Iowa Black FQ (5’ 6-FAMTM/ZENTM/3’ IB®FQ) synthesized by IDT. Combined use of three primer sets targeting different genes increased the assay accuracy and broadened the range of detection.
    multiplex, probe-based assays, ZEN, microbial, plant
  33. Insights from zebrafish and mouse models on the activity and safety of Ar-turmerone as a potential drug candidate for the treatment of epilepsy
    Orellanda-Paucar AM, Afriaknova T, et al
    PLOS One, DOI: 10.1371/journal.pone.0081634: (2013)
    cDNA synthesized from Zebrafish larvae exposed to ar-turmerone or control (vehicle) was quantified using PrimeTime qPCR Assays (primers and 5' nuclease probes). Tubulin was used as a reference gene in these experiments as it showed better expression stability compared to beta-actin (data generated in prior experiements and not shown here), and its expression levels were closer to the genes of interest.
    probe-based assays,
  34. Engineering HIV-1-resistant T-cells from short-hairpin RNA-expressing hematopoietic stem/progenitor cells in humanized BLT mice
    Ringpis G-EE, Shimizu S, et al
    PLos One, 7(12):e53492 (2012)
    Use of IDT Primers and PrimeTime® qPCR Probes for quantification of integrated vector copy number in genomic DNA from peripheral blood mononuclear cells and tissue-derived lymphocytes.
    probe-based assays
  35. Ocular Surface Extracellular DNA and Nuclease Activity Imbalance: A New Paradigm for Inflammation in Dry Eye Disease
    Sonawane S, Khanolkar V, et al
    Invest Ophthalmol Vis Sci, 53(13):8253–8263 (2012)
    Use of an IDT PrimeTime qPCR Probe in a FRET-based nuclease detection assay.
    probe-based assays
  36. Isoorientin Reverts TNF-α-Induced Insulin Resistance in Adipocytes Activating the Insulin Signaling Pathway
    Alonso-Castro AJ, Zapata-Bustos R, et. al
    Endocrinology, 153(11):5222–5230 (2012)
    Use of IDT PrimeTime qPCR Assays to monitor the expression of genes involved in the insulin signaling pathway in murine adipocytes. Probes were designed with IDT SciTools RealTime PCR Assay Tool.
    probe-based assays, RealTime PCR Assay Design Tool
  37. Development of PrimeTime-Real-Time PCR for Species Identification of Soybean Cyst Nematode (Heterodera glycines Ichinohe, 1952) in North Carolina
    Ye W
    J Nematology, 44(3):284–290 (2012)
    Development of a real-time PCR method using IDT PrimeTime qPCR Assays and ZEN Double-Quenched Probes for rapid, sensitive, species-specific and accurate identification of a parasite from mixed populations.
    probe-based assays, ZEN
  38. Gene expression profile of a persistently chronic wasting disease (CWD) prion-infected RK13 cell line
    Kim MJ, Sohn HY, et al
    J Prevent Vet med, 36:186-195 (2012)
    The expression levels of the target genes were evaluated with IDT PrimeTime qPCR Assays that included ZEN Double-Quenched Probes.
    probe-based assays, ZEN
  39. Establishment of a reverse genetics system for studying human bocavirus in human airway epithelia
    Huang Q , Deng X, et al
    PLOS, 8(8):e1002899. doi: 10.1371/journal.ppat.1002899 (2012)
    qPCR used to confirm that cloned Human bocavirus 1 (HBoV1) genome exhibits pathogenetic infection in human airway epithelia and primary B-HAE cell cultures.IDT amplicon primers and PrimeTime Dual-Labeled qPCR Probe were used. Their sequences are as follows (GenBank: JQ411251): forward primers, 5′-GCA CAG CCA CGT GAC GAA-3′ (nt 2391 to 2408); reverse primer, 5′-TGG ACT CCC TTT TCT TTT GTA GGA-3′ (nt 2466 to 2443); and PrimeTime qPCR Probe, 5′ 6FAM-TGA GCT CAG GGA ATA TGA AAG ACA AGC ATC G-3′ Iowa Black FQ (nt 2411 to 2441).
    probe-based assays, microbial
  40. Disease severity in a mouse model of ataxia telangiectasia is modulated by the DNA damage checkpoint gene Hus1
    Balmus G, Zhu M, et al
    Human Mol Genet, 21(15):3408–3420 (2012)
    Total RNA from stage 10.5 embryos was reverse transcribed and used for qRT-PCR in intercalating dye-based assays with SYBR Green. Primer pairs were designed using the IDT RealTime PCR Assay Design Tool to generate intron-spanning products of 150-200 bp. The generation of specfic PCR products was confirmed by melting curve analysis and gene electrophoresis. Each primer pair was tested iwth a logarithmic dilution of cDNA mix to generate a linear standard curve, which was used to calculate the primer pair efficiency.
    RealTime PCR Assay Design Tool, intercalating dye assays
  41. Aggregation gatekeepers modulate protein homeostasis of aggregating sequences and affect bacterial fitness
    Beerten J, Jonckheere W, et al
    Protein Engin, Design, Select, 25(7):357 – 366 (2012)
    Transcriptional activity of chaperones and proteasees was measured by RT-qPCR. Primers were designed using the IDT RealTime PCR Assay Design Tool. RT=qPCR was performed with TaqMan FAST Universal PCR Master Mix (2X) and No AmpErase UNG (Life Technologies). Assays were run on an iCycler My-iQ Single Color Real-Time PCR detection system (Bio-Rad). Gene expression was normalized against gyrA, recA, and zwf.
    RealTime PCR Assay Design Tool, bacteria
  42. MicroRNA regulation of molecular networks mapped by global microRNA, mRNA, and protein expression in activated T lymphocytes
    Grigoryev Y, Kurian S, et al
    J Immunology, 187(5):2233–2243 (2011)

    Use of a variety of assays, including IDT PrimeTime qPCR Assays with ZEN Double-Quenched Probes to measure at miRNA expression, and analyze relationship to mRNA and protein levels.

    ZEN, probe-based assays
  43. Critical selection of reliable reference genes for gene expression study in the HepaRG cell line
    Ceelen L, De Spiegelaere W, et al
    Biochem Pharmacol, 81(10):1255–1261 (2011)

    Use of a variety of tools, including IDT PrimeTime Predesigned qPCR Assays with ZEN Double-Quenched Probes to test a set of candidate reference genes in the HepaRG cell line. Note: Reference genes should always be experimentally validated in the context that they will be used, prior to the actual experiment, by the investigator. 

    PrimeTime qPCR Assay Selection Tool, probe-based assays, ZEN
  44. Identification of growth arrest and DNA-damage-inducible gene beta (GADD45beta) as a novel tumor suppressor in pituitary gonadotrope tumors
    Michaelis K, Knox A, et al
    Endocrinology, 152(10):3603–3613 (2011)

    Use of PrimeTime qPCR Assays to validate microarray array data showing suppression of GADD45β in pituitary gonadotrope tumors.

    probe-based assays
  45. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature
    Karim L, Takeda H, et. al.
    Nat Genet, 43(5):405–413 (2011)

    Use of PrimeTime qPCR Assays to identify genes involved in influencing bovine stature.

    probe-based assays
  46. A novel fluorescence-based assay for the rapid detection and quantification of cellular deoxyribonucleoside triphosphates
    Wilson P, Labonte M, et al
    Nucleic Acids Res, 1(39):e112 (2011)

    A novel method using PrimeTime qPCR Assays with ZEN Double-Quenched Probes to measure cellular dNTP levels. The authors show that amount of a limiting dNTP is directly proportional to the amount of fluorescence observed, and that ZEN Double-Quenched Probes provided the necessary sensitivity for the assay compared to a single quenched design.

    probe-based assays, ZEN