21_NG_ProductOverview_HeaderIcon_qPCR

PrimeTime™ qPCR Probe Assays

Primer and probe premixed sequences for analyzing gene expression in any species using fluorescently labeled 5′ nuclease probes

PrimeTime qPCR Probe Assays consist of a primer pair and fluorescently labeled 5′ nuclease probe. Obtain predesigned sequences for human, mouse, or rat for easy selection based on multiple criteria such as exon location and number of transcripts. Create custom assays for any sequence from any species using the PrimerQuest™ Tool.

Ordering

  • Predesigned sequences will achieve 90% efficiency or better, or we will replace the assay with an alternative design free of charge.
  • Size and scale options available for digital PCR (dPCR) platforms
  • Pair with high-performance ZEN™ or TAO™ to create a double-quenched probe.
  • Select a primer:probe ratio from 2:1 to 4:1 with no additional charge
  • Receive primers and probe sequences with all orders
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PrimeTime qPCR Probe Assays in tubes (1 probe/2 primers)

Available in various sizes, premixed, and shipped dried down.

5' Reporter Dye(s) / Emission (nm)3' QuencherMini (100-rxn)Standard (500-rxn)XL (2500-rxn)
ATTO 425
483
ZEN / Iowa Black™ FQ$201.00 SGD$379.00 SGD$881.00 SGD
FAM
520
ZEN / Iowa Black FQ$160.00 SGD$300.00 SGD$753.00 SGD
Black Hole Quencher 1$201.00 SGD$379.00 SGD$881.00 SGD
TAMRAN/A$300.00 SGD$753.00 SGD
TET
539
ZEN / Iowa Black FQN/A$300.00 SGD$753.00 SGD
YAK
551
ZEN / Iowa Black™ FQ$311.00 SGD$573.00 SGD$1,430.00 SGD
SUN
554
ZEN / Iowa Black™ FQ$160.00 SGD$300.00 SGD$753.00 SGD
Iowa Black FQ$160.00 SGD$300.00 SGD$753.00 SGD
HEX
555
ZEN / Iowa Black™ FQ$160.00 SGD$300.00 SGD$753.00 SGD
Black Hole Quencher 1$201.00 SGD$379.00 SGD$881.00 SGD
5' Texas Red®-X
617
Iowa Black RQ$201.00 SGD$379.00 SGD$881.00 SGD
Black Hole Quencher 2$228.00 SGD$444.00 SGD$1,056.00 SGD
Cy5
668
Iowa Black RQN/A$379.00 SGD$881.00 SGD
TAO / Iowa Black RQ$201.00 SGD$379.00 SGD$881.00 SGD
Black Hole Quencher 2$228.00 SGD$444.00 SGD$1,056.00 SGD
ATTO 647
662
Iowa Black RQ$201.00 SGD$379.00 SGD$881.00 SGD
Black Hole Quencher 2$228.00 SGD$444.00 SGD$1,056.00 SGD
Cy5.5
706
Black Hole Quencher 3$311.00 SGD$573.00 SGD$1,430.00 SGD

Probes/primers supplied in the following ratios: 0.5/1.0 nmol (Mini); 2.5/2.5–10 nmol (Standard); 12.5/12.5–50 nmol (XL). You may specify the primer-to-probe ratio (except for PrimeTime Mini).

* Predesigned assays are available for human, mouse, and rat targets.

PrimeTime qPCR Probe Assays in 96-well plates (1 probe/2 primers)

Available in various sizes, premixed, and shipped dried down.

5' Dye / Emission (nm)3' QuencherMini (100-rxn)Standard (500-rxn)XL (2500-rxn)
FAM 520ZEN / Iowa Black FQ*$130.00 SGD$204.00 SGD$596.00 SGD
TAMRAN/A$265.00 SGD$689.00 SGD
HEX 555ZEN / Iowa Black FQ*N/A$265.00 SGD$689.00 SGD
TET 539ZEN / Iowa Black FQ*N/A$265.00 SGD$689.00 SGD
Cy5 668Iowa Black RQN/A$265.00 SGD$689.00 SGD

Probes/primers supplied in the following ratios: 0.5/1.0 nmol (Mini); 2.5/2.5–10 nmol (Standard); 12.5/12.5–50 nmol (XL). You may specify the primer-to-probe ratio (except for PrimeTime Mini). A minimum order of 24 assays is required per plate.

Available dye and quencher combinations for PrimeTime qPCR 5′ Nuclease Assays in plate well format

5' dye3' quencherMiniStandardXL
FAMZEN™/Iowa Black FQ*
FAMTAMRA
HEXZEN/Iowa Black FQ*
TETZEN/Iowa Black FQ*
Cy® 5Iowa Black RQ

Key: • = available; – = not available

* ZEN/Iowa Black™ FQ is a Double-Quenched Probe, which provides superior performance compared to traditional single-quenched probes. For more information download the PrimeTime Custom qPCR Probes Flyer.

50% off

2 PrimeTime™ Probe Assays 

Maximize your savings, receive 50% off when you buy 2 PrimeTime™ qPCR Probe Assays of the same scale (mini, standard, or XL)

Expires: June 30, 2025

Promo code:

2forOneAssays

Apply code

Product details

  • PrimeTime qPCR Probe Assays consist of a forward primer, a reverse primer, and a qPCR probe all delivered in a single tube or 96-well plate
  • Available in 18 dye–quencher combinations and 3 reaction scales

Predesigned PrimeTime qPCR Probe Assays are designed using IDT’s proprietary algorithm and optimized for melting temperature (Tm), single nucleotide polymorphism (SNP) avoidance (using up-to-date NCBI RefSeq data), minimized off-target amplification, splice variant recognition, and secondary structure prediction.

For commonly studied pathways in human, mouse, and rat, we offer suggested gene sets—available in the Resources section below—that can be loaded into the PrimeTime plate ordering system for fast, efficient, and high-throughput qPCR setup.

Transparency with every order

Orders include primer sequences to help labs enhance publication credibility by adhering to MIQE guidelines, identify and avoid SNPs, facilitate multiplex experiment design, assist with data interpretation and troubleshooting, and enable transcript validation.

Product data

PrimeTime qPCR Probe Assays provide reliable results

To demonstrate the performance of different dye-quencher combinations, we tested a dilution series to evaluate PCR efficiency and R2 values across all dye-quencher combinations available (Figure 1).

Dye-quencher combination FAM/ZEN/Iowa Black FQ Sun/ZEN/Iowa Black FQ HEX/ZEN/Iowa Black FQ TET/ZEN/Iowa Black FQ Cy5/TAO/Iowa Black RQ
Amplification curve Amplification Curve - FAM / Iowa Black FQ Amplification Curve - FAM / TAMRA Amplification Curve - HEX / Iowa Black FQ Amplification Curve - TET / Iowa Black FQ Amplification Curve - Cy5/Iowa Black RQ
Standard curve Standard Curve - FAM / Iowa Black FQ Standard Curve - FAM / TAMRA Standard Curve - HEX / Iowa Black FQ Standard Curve - TET / Iowa Black FQ Standard Curve - Cy5/Iowa Black RQ
Efficiency 97.4 99.7% 98.4% 97.2% 95.0%
Correlation coefficient (R²) 0.997 0.998 0.997 0.998 0.999

Figure 1. Demonstrated assay performance with multiple dye–quencher combinations. A gBlocks Gene Fragment dilution series of the HPRT gene was used to test different dye-quencher combinations. The data show PCR efficiency and R2 values close to 1 across all dye/quenchers available for PrimeTime qPCR Assays. All reactions were run using IDT’s PrimeTime Gene Expression Master Mix under standard two step cycling conditions 95°C for 3 min, (95 °C for 15 sec + 60°C for 1 min) x 40 on the QuantStudio™ 7 Flex (Thermo Fisher Scientific) 386 well format. Reactions were 10 µL in volume and contained 500 nM primers and 250 nM probe. The PrimeTime Gene Expression Master Mix was used with low ROX reference dye.

Compatibility with commercially available master mixes

To determine the success of PrimeTime qPCR Probe Assays with commercially available master mixes, we tested 5 different master mixes over a dilution series of 6 orders of magnitude (Figure 2). The PrimeTime qPCR Probe Assays had efficiency close to 100% across many commercially available master mixes. We have also developed the PrimeTime Gene Expression Master Mix for use with PrimeTime probe-based assays in two-step RT-qPCR.

Product Qiagen QuantiNova Probe PCR Kit Thermo Fisher Scientific  TaqMan Fast Advanced Bio-Rad Sso Advanced Aligent Stratagene Brilliant II® Takara Premix Ex Taq IDT Gene Expression Master Mix
Amplification curve Amplification Curve - Qiagen QuantiTect Probe PCR Kit Amplification Curve - AB TaqMan® Gene Expression Master Mix Amplification Curve - Bio-Rad iTaq™ Supermix with ROX Amplification Curve - Stratagene Brilliant II® QPCR Master mix Amplification Curve - Invitrogen Express qPCR SuperMix Amp-Curve-IDT-Gene-Expression-Master-Mix
Standard curve Standard Curve - Qiagen QuantiTect Probe PCR Kit Standard Curve - AB TaqMan® Gene Expression Master Mix Standard Curve - Bio-Rad iTaq™ Supermix with ROX Standard Curve - Stratagene Brilliant II® QPCR Master mix Std Curve - Takara Premix Ex Taq Std Curve - IDT Gene Expression Master Mix
Efficiency 102.1% 98.6% 99.8% 98.0% 101.8% 99.1%
Correlation coefficient (R²) 0.998 0.998 0.996 0.996 0.999 0.998

Figure 2. Successful amplification of PrimeTime qPCR Probe Assays with various commercial qPCR master mixes. A 10-fold dilution series over 6 orders of magnitude (1 x 106 to 1 x 101 copies) was created for the HPRT1 transcript. The standard curves were generated by running the assay with the indicated commercial master mixes. The samples were run on a Thermo Fisher Scientific QuantStudio™ 7 Flex instrument under standard cycling conditions for 40 cycles. The data shows greater than 90% efficiency and correlation coefficients greater than 0.99 for all tested qPCR master mixes.

 

Low variability between assay lots and across assay scales

PrimeTime qPCR Probe Assays have low variability from lot to lot and across scales, which supports your research needs for re-ordering consistent assays and for transitioning from discovery or validation applications to screening. We tested 5 genes from 2 lots each of mini, standard, and XL PrimeTime qPCR Probe Assays. The assays showed consistency between lots and across all 3 scales with negligible Cq variation (Figure 3).

Gene ID
  HPRT1 PGK1 RPLP0 UBC WDR3
Mini Replicate 1 27.1 23.7 21.1 21.8 26.7
Replicate 2 27.1 23.7 21.1 21.8 26.6
Standard Replicate 1 27.2 23.7 21.1 21.6 26.5
Replicate 2 26.9 23.5 21.1 21.6 26.4
XL Replicate 1 27.1 23.5 21.0 21.3 26.4
Replicate 2 27.0 23.5 21.1 21.4 26.3
Amplification curves Amplification Curve - TNFRSF1A Amplification Curve - PDK1 Amplification Curve - JAK2 Amplification Curve - E2F1 Amplification Curve - TEC

Figure 3. PrimeTime qPCR Probe Assays are consistent from lot to lot and across scales. Reverse transcription of qPCR Human Reference total RNA (Agilent) was performed using oligo(dT), random hexamers, and SuperScript® II (Thermo Fisher Scientific). Each qPCR reaction contained 50 ng of cDNA. All assays were run in duplicate on the CFX384 Touch Real-Time PCR system (BioRad) for 45 cycles using the PrimeTime Gene Expression Master Mix. The Cq values for the 2 replicates are shown. Assays for 5 genes were formulated as PrimeTime Mini, Standard, and XL qPCR Assays.

Dynamic range down to 10 copies

To show the dynamic range for PrimeTime qPCR Probe Assays, we tested a dilution over 6 orders of magnitude down to 10 copies per reaction (Figure 4). All dilutions tested produced highly consistent results.

Figure 4. Dynamic range (6 logs) down to 10-copies. An HPRT PrimeTime qPCR Probe Assay was analyzed by utilizing a gBlock Gene Fragments dilution series and a no template control (NTC). The data shown illustrates 6 logs of dynamic range and assay down to 10 copies per reaction. The efficiency of the assay calculated from the standard curve is 97.6% with a correlation coefficient of 0.9991.

PrimeTime qPCR Probe Assays excel with fast-cycling protocols

Fast cycling allows for higher throughput and faster access to results. Unfortunately, researchers often have to sacrifice performance for speed. PrimeTime qPCR Probe Assays were tested using the PrimeTime Gene Expression Master Mix, which allows run times as short as 45 minutes. These results were compared to 30 matched, inventoried assays from a competitor.

  • Greater low copy input limit─twelve out of the sixteen PrimeTime qPCR Probe Assays had lower Cq values compared to matched, inventoried assays from a competitor.
  • No sacrifice in efficiency─all PrimeTime Assays maintained efficiencies of 90–105%.

Lower mean Cq values

Sixteen assays from a competitor were compared to an equal number of PrimeTime qPCR 5' Nuclease Assays. To ensure the assays were comparable, the PrimeTime Assays and Competitor assays were selected to span the same exon boundary of each gene. The reactions were run with the PrimeTime Gene Expression Master Mix and identical thresholds were set for all runs (Figures 5).

Figure 5. PrimeTime qPCR Assays have consistently lower mean Cq values for the same target. PrimeTime qPCR Assays were compared to matched Competitor assays using five, 4-fold dilutions of cDNA and the PrimeTime Gene Expression Master Mix. The reactions were run on the CFX384 Touch Real-Time PCR system (BioRad) for 45 cycles with the following PCR cycling conditions: 2 min 50°C; 10 min 95°C; 45 x (15 sec 95°C, 1 min 60°C). Identical thresholds were set for all runs for comparison across assays.

Higher qPCR efficiency

qPCR efficiency was compared using 30 PrimeTime qPCR Probe Assays and Competitor A assays (Figure 6). Again, the PrimeTime qPCR Assays showed a higher average qPCR efficiency than Competitor assays. In addition, the overall distribution of qPCR efficiency was narrower and higher than that for Competitor assays.

Figure 6. PrimeTime qPCR Assays have higher average qPCR efficiency and a smaller distribution range than Competitor assays. PrimeTime qPCR Assays were compared to matched Competitor assays using five, 4-fold dilutions of cDNA and the PrimeTime Gene Expression Master Mix. The reactions were run on the CFX384 Touch Real-Time PCR Detection System (BioRad) with the following PCR cycling conditions: 2 min 50°C; 10 min 95°C; 45 x (15 sec 95°C, 1 min 60°C). Identical thresholds were set for all runs for comparison across assays.

Resources

Gene sets for common pathways

Frequently asked questions

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