PrimePCR™ PCR Primers, Assays, and Arrays


Real-time PCR primer assays consist of unlabeled PCR primer pairs for use with dye-based chemistry such as SYBR® Green or EvaGreen®. Probe assays for real-time PCR and Droplet Digital™ PCR include PCR primers and a dual-labeled fluorescent probe with your choice of fluorophore.

Get assays designed for Droplet Digital PCR Get assays designed specifically
for Droplet Digital PCR

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Order custom PCR primer or probe assays Order custom PCR primer or
probe assays

Use this option if you already have your primer/probe sequences.

PrimePCR Search Tools

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          PrimePCR Lookup Tool

          Use the PrimePCR lookup tool to find assays and arrays for your genes of interest. Launch Lookup Tool PrimePCR Lookup Tool
          PrimePCR™ Lookup Tool

          Use the PrimePCR lookup tool to find assays and panels for your genes of interest.

          Launch PrimePCR Lookup Tool


          Create a Custom PCR Plate

          Design a custom 96-well or 384-well PCR plate. Configure New Plate Create a Custom PCR Assay

          More Assay Search Tools

          Find a PrimePCR Array
          Find a predesigned PCR plate for your biological pathway or disease of interest. Find a Pathway Plate
          Find a ddPCR Assay
          Choose your application, enter your target, and let our tool find the right assay for you. Find a ddPCR Assay
          Droplet Digital™ PCR Assays

          Pricing for PrimePCR Droplet Digital PCR assays is based on assay type and the number of reactions.

          Discount applies to bulk orders of the same catalog number and is taken off the list price.

          Bulk discounts are shown below; download the pricing flyer for full details.

          ddPCR Assays

          5 or more assays

          25% off

          Why PrimePCR?

          Design and Validation of Real-Time PCR Primers

          Bio-Rad collaborated with Biogazelle, leaders in real-time PCR research, to design and experimentally validate PCR primers for gene expression assays across the human and mouse transcriptomes. All PCR primers were designed to meet stringent performance standards following the MIQE guidelines (minimum information for publication of quantitative real-time PCR experiments; Bustin et al. 2009).

          Assay Performance Standards

          Sensitivity Accurate detection of 20 copies
          Specificity Amplicon sequence validated with next generation sequencing (NGS). Minimal primer dimer formation and genomic DNA cross reactivity.
          Amplification Efficiency 90–110%
          Linear Dynamic Range Minimum of six orders of magnitude. Detection of a synthetic template standard curve from 20 to 20 million copies.
          R2 >0.99

          These DNA primer pairs were designed by prioritizing the gene regions most commonly found in transcript variants. Strict design criteria were used to ensure optimal real-time PCR results for each target:

          • Target regions without SNPs
          • PCR primer pairs annealing across intron/exon junctions when possible
          • No secondary structure in primer annealing sites
          • Maximum number of transcript isoforms detected
          • PCR primers compatible with standard assay conditions

          Every PCR primer pair was experimentally validated using Bio-Rad’s iScript™ advanced cDNA synthesis kit and SsoAdvanced™ SYBR® Green supermix. PrimePCR assay design and validation are fully described in the following publication.

          PrimePCR Assays: Meeting the MIQE Guidelines by Full Wet-lab Validation

          Pathway Curation

          Thomson Reuters provided interactive pathway maps for 260 canonical pathways. Each pathway belongs to one or more general biological categories such as cancer. The pathway maps illustrate protein interactions and regulation to provide a comprehensive picture of signaling and disease processes. The selected pathways were used to design panels of real-time PCR primers tailored for the top-ranked genes for differential gene expression analysis. Each gene target within a pathway was assigned a score based on the frequency of differential expression and its research significance. The resulting scores were used to select the assays included in the corresponding real-time PCR pathway panel.

          PrimePCR Pathway Analysis: Pathway Curation and Real-Time PCR Panel Design Strategy

          Control and Reference Assays for Real-Time PCR

          Control assays and synthetic DNA templates were designed to facilitate the assessment of the key experimental factors impacting your real-time PCR results.

          DNA Contamination Control Assay
          Use the PrimePCR DNA contamination control assay to determine if genomic DNA (gDNA) is present in a sample at a level that may affect PCR results. This assay may also be used to compare relative levels of gDNA contamination present in different samples to determine if PCR results may be affected.

          Positive PCR Control Assay
          Use the PrimePCR positive control assay to qualitatively assess the performance of a PCR reaction associated with a single sample. This assay may also be used to compare the relative performance of PCR reactions associated with different samples.

          RNA Quality Assay
          Use the PrimePCR RNA quality assay to determine if RNA integrity may adversely affect PCR results for a single sample. This assay may also be used to compare relative RNA integrity among different samples to determine how PCR results might be affected.

          Reverse Transcription Control Assay
          Use the PrimePCR reverse transcription control assay to qualitatively assess the performance of the reverse transcription reaction associated with a single sample. This assay may also be used to compare the relative performance of the reverse transcription reactions associated with different samples.

          Reference Gene Assays
          Reference genes are used in relative gene expression analysis to normalize for variation in the amount of input messenger RNA (mRNA) among samples. To ensure accurate quantitation, it is important to include one or more reference genes exhibiting constant expression levels under the experimental conditions. To streamline reference gene selection, we offer PCR primers for a set of commonly used reference genes that can be used individually, easily screened using our preplated 96-well and 384-well reference panels or added to custom-designed plates.

          Show Reference Gene Assays
          View Reference Gene Assay Panels

          PrimePCR Assay Selection Guide


          Real-Time PCR Assays

          Droplet Digital PCR Assays

          Organisms Human, mouse, rat, yeast, rhesus monkey,
          arabidopsis, dog, chicken, zebrafish, cow, pig, rabbit
          Human, mouse, rat
          Assay Chemistry Dye-based and probe assays
          Applications Gene expression
          Copy number variation
          Mutation detection
          Gene expression
          Formats Individual assays
          96- and 384-well predesigned plates*
          96- and 384-well custom plates*
          Individual assays

          * Probe assays are not available in plates

          PCR Primer and Probe Assays for Real-Time PCR

          Our real-time PCR primers were designed in collaboration with leading experts in real-time PCR research. Every PCR primer pair has been experimentally validated to ensure optimal assay performance. For more information on the validation of the DNA primer pairs, see Bulletin 6262, PrimePCR Assay Validation.

          Our fluorescently labeled oligonucleotide probes were designed to enable multiplexing. These 5' nuclease probes were designed for maximum specificity and transcript coverage. qPCR probe assays are available with a FAM, HEX, TEX615, Cy5, or Cy5.5 fluorophore.

          Real-time PCR assays are available in the following formats:

          • Predesigned primer and probe assays — gene expression assays for the human and mouse genomes
          • Custom oligonucleotides — design your own PCR primer or probe assay
          • Customizable 96- and 384-well platesuse the custom plate configurator to conveniently design a PCR plate
          • Predesigned PCR Arrays — select from a wide variety of disease- and pathway-specific arrays
          • PreAmp assays — 1,000-fold unbiased target-specific preamplification of limited nucleic acid

          Controls and Reference Assays are available to facilitate assay normalization and control:

          • Experimental Controls — for evaluating reverse transcription performance, RNA quality, genomic DNA contamination, and PCR reaction performance
          • Reference Gene Assays — for relative gene expression analysis to normalize for variation in the amount of input messenger RNA (mRNA) between samples
          • DNA templates — serve as a positive real-time PCR control for the corresponding gene assay

          All real-time PCR assays and arrays can be used with CFX real-time PCR detection systems and data analysis software, streamlining PCR data collection and analysis.

          Probe Assays for Droplet Digital PCR

          Droplet Digital PCR (ddPCR™) technology provides an absolute measure of target DNA molecules with unrivaled accuracy, precision, and sensitivity, accelerating discovery and enabling new research strategies for inherited disorders, cancer, and infectious disease. Probe assays for the QX200™ Droplet Digital PCR system enable the fine quantitative discrimination required to resolve small fold changes without a standard curve. ddPCR probe assays are available with a FAM or HEX fluorophore.

          For more information, see Bulletin 6512.

          ddPCR assays are available in the following formats:

          • Predesigned mutation detection probe assays — for human samples
          • Predesigned copy number variation (CNV) probe assays — for human samples
          • Custom oligonucleotides — design your own ddPCR probe assay

          PrimePCR assays, plates, and controls have a guaranteed shelf life of 12 months when stored at 4°C.

          PrimePCR™ Analysis Software

          PrimePCR™ Analysis Software

          Our custom data analysis software enables gene expression analysis of PrimePCR data generated on any real-time PCR instrument. Analysis options include bar chart, clustergram, scatter plot, volcano plot, and heat map analysis.

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          PrimePCR™ Analysis Software

          Data analysis software that enables gene expression analysis of PrimePCR data generated on any real-time PCR instrument. Analysis options include bar chart, clustergram, scatter plot, volcano plot, or heat map analysis.

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          Number Description Options
          10000088666 Instruction Manual, PrimePCR Assays, Panels, and Controls, Ver G Click to download
          10042030 PrimePCR™ PreAmp Assay Quick Guide, Rev A Click to download
          10039761 PrimePCR™ Assays Quick Guide, Ver B Click to download
          6763 Gene Expression Real-Time PCR Workflow Flier Click to download [ Add to Cart (Free) ]
          6290 PrimePCR Assays and Panels Brochure, Rev D Click to download
          6595 PrimePCR™ Assays and Panels for Real-Time PCR Brochure, Rev A Click to download [ Add to Cart (Free) ]
          6512 PrimePCR Assays for Droplet Digital PCR Brochure, Rev A Click to download [ Add to Cart (Free) ]
          6629 High-Throughput Real-Time PCR Solutions Brochure, Ver B Click to download
          10041702 PrimePCR™ ddPCR™ Gene Expression Assays (EvaGreen) Product Insert, Rev A Click to download
          10048730 PrimePCR™ ddPCR™ Gene Expression Probe Assays Product Insert, Rev A Click to download
          10033173 ddPCR Copy Number Variation Assays, Validated, Product Insert Click to download
          10033487 ddPCR Mutation Detection Assays, Validated, Product Insert Click to download
          10047489 ddPCR Mutation Detection Assays Product Insert Click to download
          6262 PrimePCR Assays: Meeting the MIQE Guidelines by Full Wet-Lab Validation, Rev B Click to download
          6263 PrimePCR Pathway Analysis: Pathway Curation and Real-Time PCR Panel Design Strategy, Rev B Click to download
          6679 Droplet Digital™ PCR: Multiplex Screening of KRAS Mutations in Cell-Free DNA Colorectal Cancer Samples Application Note, Rev A Click to download
          6634 A Fast Semi-Automated Quantitative PCR Method for Monitoring Differential Gene Expression for Drug Target Discovery, Ver B Click to download
          6734 PrimePCR™ Publications List, Rev A Click to download
          6777 Protocol for Single Cell Gene Expression Profiling by Multiplex RT-qPCR Click to download
          6816 Protocol for Multiplex RT-qPCR Analysis Using PrimePCR™ Assays, Ver A Click to download
          10000065278 ddPCR™ NHEJ Genome Edit Detection Assays, Ver A Click to download
          10000065279 ddPCR™ HDR Genome Edit Detection Assays, Predesigned, Ver A Click to download
          10000065281 ddPCR™ HDR Genome Edit Detection Assays, Ver A Click to download

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