PCR Primers and Panels

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PrimePCR - Real-Time PCR Primers for Gene Expression Assays

Why PrimePCR?

Assay Design and Validation
Assay Design and Validation

We have collaborated with Biogazelle, leaders in real-time PCR, to design and experimentally validate SYBR® Green-based gene expression assays for the human and mouse transcriptome. Primer pairs for each gene were designed by prioritizing gene regions most commonly occurring in transcript variants. Every assay was wet-lab validated using iScript™ advanced cDNA synthesis kit and SsoAdvanced™ SYBR® Green supermix.

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

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

Pathway Curation
Pathway Curation

Bio-Rad Laboratories has partnered with GeneGo, a Thomson Reuters business and leading provider of systems biology tools, to offer a complete pathway solution for real-time PCR-based gene expression analysis. As part of the collaboration, 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 curated pathways were also used to design panels of real-time PCR assays specifically tailored to the top ranked gene targets for differential gene expression analysis. Each gene target within a pathway was assigned a score based on frequency of differential expression and popularity in scientific research both historically and currently. The resulting scores were used to rank and select which assays were included on the corresponding real-time PCR pathway panel.

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

Controls and References
Controls and References
Controls

Control assays and synthetic DNA templates are designed to aid in assessing the key experimental factors that may be impacting your real-time PCR results.

DNA Contamination Control Assay
The PrimePCR DNA contamination control assay is designed to determine if genomic DNA (gDNA) is present in a sample at a level that may affect PCR results. The 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
The PrimePCR positive control assay is designed to qualitatively assess the performance of a PCR reaction associated with a single sample. The assay may also be used to compare the relative performance of the PCR reactions associated with different samples.

RNA Quality Assay
The PrimePCR RNA quality assay is designed to determine if RNA integrity may adversely affect PCR results of a single sample. The assay may also be used to compare the relative RNA integrity between different samples in order to determine if PCR results may be affected.

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

References Gene Assays
Reference genes are used in relative gene expression analysis to normalize for variation in the amount of input messenger RNA (mRNA) between samples.  For accurate quantitation, it is important to use one or more reference genes that are shown not to change expression as a result of the experimental treatment or condition.  To aid in this, we have suggested a set of commonly used reference genes that can be used individually, easily screened using our pre-plated 96-well and 384-well reference panels, or added to custom designed plates. 

Show Reference Gene Assays
View Reference Gene Assay Panels


Search to Order PrimePCR Assays, Panels, and Controls
PrimePCR Primer Assays for Real-Time PCR biological signaling pathway maps

More than 300 expertly curated biological pathway panels for a variety of real-time PCR instruments.

Browse Pathways
PrimePCR Primer Assays for Real-Time PCR custom 96 and 384 well PCR plates

Design a 96- or 384-well plate with PrimePCR or custom assays.


Create Custom Plate
PrimePCR Primer Assays for Real-Time PCR custom primer pair sequence for SYBR Green gene expression

Enter your own primer sequences to create a custom assay.


Create Custom Assay

PCR Primers and Panels

Bio-Rad's PCR primers comprise genome-wide real-time PCR assays for the human and mouse genomes. 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

PCR Primer Assay Performance Validation

Our 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.

PCR Primers for the Human and Mouse Genomes are Available in Different Formats

  • Predesigned assays — choose from genome-wide PCR primer pairs for SYBR® Green-based gene expression analysis
  • Custom oligonucleotides – design your own PCR primers
  • Customizable 96- and 384-well plates – use the custom plate configurator to conveniently design a plate format for your exact needs
  • Predesigned pathway panels – select from a wide variety of disease- and pathway-specific panels

Controls and Reference Assays

  • Experimental controls – for evaluating reverse transcription performance, RNA quality, genomic DNA contamination and PCR reaction performance
  • Reference gene panels – for the identification of the best reference gene assays for your sample
  • DNA templates – serve as a positive real-time PCR control for the corresponding gene assay

Full Integration with CFX Manager™ Software

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

Related Products

Bio-Rad offers a complete workflow solution for real-time PCR including:

More Information

To ensure that your qPCR reactions are reproducible and reliable, follow our step-by-step design and optimization protocols. We also provide insights into the analysis of qPCR data and troubleshooting real-time PCR reactions. For detailed information on PrimePCR Assays, download bulletin 6290.

Number Description Download
6252 Reagent Comparison Guide for Real-Time PCR Brochure, Rev C Click to download
10026370 Instruction Manual, PrimePCR Assays, Panels, and Controls, Rev B 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
6290 PrimePCR Assays and Panels Brochure, Rev A Click to download