RT2 Profiler PCR Arrays

For pathway-focused gene expression analysis using laboratory-verified assays

Features

  • Profile 84 or 370 related genes simultaneously
  • Expert-designed panels target the most relevant genes
  • Laboratory-verified assays eliminate tedious optimization
  • Simple procedure enables routine use with any real-time PCR instrument
  • Complimentary online tools make data analysis quick and easy

Products

RT2 Profiler PCR Arrays are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.
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RT2 RNA QC PCR Array

Cat. No. / ID: 330291

RT2 Profiler QC Array
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RT2 Profiler PCR Array

Cat. No. / ID: 330231

RT2 Profiler PCR Array

Product Details

RT² Profiler PCR Arrays enable quick, reliable gene expression analysis of 170+ pathways, allowing researchers to spend less time at the bench and more time interpreting results. The arrays are pathway-focused panels of laboratory-verified qPCR assays, with integrated, patented controls to ensure a successful experiment every time. PhD-trained application specialists are available to provide technical support for the arrays, and each array can also be modified to suit unique experimental needs. For biomarker discoveries, we offer Pathway Plus PCR arrays and all arrays listed below for the Fluidigm BioMark Real-Time PCR System. 

Performance

Sensitivity

With the sensitivity of the RT2 First Strand Kit, as little as 1 ng or as much as 5 µg of total RNA per array plate provides greater than 80% present call rates (see figure " Positive results with as little as 25 ng RNA").

Reproducibility

The complete PCR array system demonstrates strong correlations across technical replicates, lots, and instruments with average correlation coefficients >0.99, ensuring reliable detection of differences in expression between biological samples (see figure " High reproducibility among different users").

Specificity

The PCR array system, with high-quality input RNA, yields single bands of the predicted size without primer-dimers or other secondary products, therefore providing the highly accurate real-time PCR results (see figure " A single gene-specific product in every reaction").

Uniform PCR amplification efficiency

Uniform PCR amplification efficiency is required for the PCR array technology to allow accurate comparisons of gene expression across all genes and all samples. The unique combination of our proprietary primer design algorithm and rigorous testing of every primer assay guarantees the high performance of every primer assay on PCR arrays (see figure " PCR arrays yield highly accurate results").

A guaranteed system

RT² Profiler PCR Arrays are tested and optimized in combination with the RT² SYBR Green qPCR Mastermixes and the RT² First Strand Kit. This testing means that RT² Profiler PCR Array performance is guaranteed when all three of these components are used together.

See figures

Principle

RT2 Profiler PCR Arrays are reliable tools for analyzing the expression of a focused panel of genes. Each 96-well plate, 384-well plate or 100-well disc PCR array includes SYBR® Green-optimized primer assays for a thoroughly researched panel of relevant, pathway- or disease-focused genes. RT2 Profiler PCR Arrays can also be customized to contain a panel of genes tailored to your specific research interests. The high-quality primer design and RT2 SYBR® Green qPCR Mastermix formulation enable the PCR array to amplify 96 or 384 different gene-specific products simultaneously under uniform cycling conditions.

This combination provides the RT2 Profiler PCR Array with the specificity and the high amplification efficiencies required for accurate real-time SYBR® Green results. PCR arrays are easy to use in any research laboratory.

RT2 Profiler PCR Arrays are sensitive enough for use with RNA prepared from regular samples (0.1–5 µg RNA), FFPE samples, and small samples (1–100 ng RNA).

Procedure

Simply mix the cDNA template with the appropriate ready-to-use PCR mastermix, aliquot equal volumes to each well of the same plate, and then run the real-time PCR cycling program (see flowchart " Simple procedure"). RT2 Profiler PCR Arrays are compatible with all QIAGEN, ABI, Bio-Rad, Eppendorf, Roche, and Stratagene instruments.

Flexible layout and controls

RT2 Profiler PCR Arrays are available in 96-well plate, 384-well plate, and 100-well disc formats, and are used to monitor the expression of 84 or 370 genes related to a disease state or pathway, plus 5 housekeeping genes. Each RT2 Profiler PCR Array also includes control elements for:

  • Data normalization
  • Genomic DNA contamination detection
  • RNA sample quality 
  • General PCR performance
Easy-to-use data analysis

Data can be analyzed using an easy-to-use Excel-based data analysis template or Web-based software. Data analysis is based on the ΔΔCT method with normalization of the raw data to either housekeeping genes.

See figures

Applications

RT² PCR Profiler Arrays can be used in all areas of biological and medical research, including:

  • Cancer Inflammation and cytokine profiling
  • Stem cells
  • Neuroscience
  • Signal transduction pathways
  • Cell adhesion and cell migration
  • Biomarker screening and Validation

Supporting data and figures

Resources

Brochures & Guides (3)
Simultaneously profile mRNA, miRNA and lncRNA using a simple, complete workflow
Safety Data Sheets (1)
Download Safety Data Sheets for QIAGEN product components.
Download Files (3)
For analyzing gene expression data from RT2 Profiler PCR Arrays 
Data analysis file for RT² Profiler PCR Array Housekeeping Genes
Catalog number- 330231
Pathway number- PAXX-000
RNA QC Data Analysis
XLS (484KB)

Data analysis file for RT² ProfilerRT² Profiler™ PCR Array RT2 RNA QC
Catalog number- 330231
Pathway number- PAXX-999

Scientific Posters (1)
Poster for download
Kit Handbooks (1)
For pathway-focused gene expression profiling using real-time RT-PCR
Instrument Technical Documents (2)
For gene expression and genomic analysis
For pathway-focused gene expression analysis

Publications

CD8 T cells use IFN-γ to protect against the lethal effects of a respiratory poxvirus infection.
Goulding J; Abboud G; Tahiliani V; Desai P; Hutchinson TE; Salek-Ardakani S;
J Immunol; 2014; 192 (11):5415-25 2014 Apr 18 PMID:24748494
Sphingosine kinase 1 expressed by endothelial colony-forming cells has a critical role in their revascularization activity.
Poitevin S; Cussac D; Leroyer AS; Albinet V; Sarlon-Bartoli G; Guillet B; Hubert L; Andrieu-Abadie N; Couderc B; Parini A; Dignat-George F; Sabatier F;
Cardiovasc Res; 2014; 103 (1):121-30 2014 Apr 17 PMID:24743591
Adipose tissue insulin resistance due to loss of PI3K p110α leads to decreased energy expenditure and obesity.
Nelson VL; Jiang YP; Dickman KG; Ballou LM; Lin RZ;
Am J Physiol Endocrinol Metab; 2014; 306 (10):E1205-16 2014 Apr 1 PMID:24691033
FBXW7 mutations in melanoma and a new therapeutic paradigm.
Aydin IT; Melamed RD; Adams SJ; Castillo-Martin M; Demir A; Bryk D; Brunner G; Cordon-Cardo C; Osman I; Rabadan R; Celebi JT;
J Natl Cancer Inst; 2014; 106 (6):dju107 2014 May 16 PMID:24838835
β-Carotene-9',10'-oxygenase status modulates the impact of dietary tomato and lycopene on hepatic nuclear receptor-, stress-, and metabolism-related gene expression in mice.
Tan HL; Moran NE; Cichon MJ; Riedl KM; Schwartz SJ; Erdman JW Jr; Pearl DK; Thomas-Ahner JM; Clinton SK;
J Nutr; 2014; 144 (4):431-9 2014 Feb 19 PMID:24553694

FAQ

What is the best approach for determining where to set the CT threshold when you have >15 samples? Is it best to go through all of them, looking for a range of best fit, and then just choose one value that fits all of them?
The best way to set the threshold is to make sure that your PPC values are between 18 and 22. I would look my first PCR Array, set it so that the PPC is at 20, and see if the same threshold fits for the rest of the arrays.
FAQ ID -2705
How many housekeeping genes are included in each PCR Array?
Each PCR Array has 5 housekeeping genes. You can use one or an average of the most stable ones to do data analysis.
FAQ ID -2704
Are primers available that only detect mitochondrial DNA encoded genes and not nuclear genomic DNA encoded genes?
There are less than a dozen genes encoded by the mitochondrial genome (all other mitochondrial proteins are encoded by nuclear genes), and they are all transcribed as one transcript (just like any prokaryote), so distinguishing the expression of individual genes by real-time RT-PCR is not possible.
FAQ ID -2680
What is the RT² Profiler PCR Array?
The RT² Profiler PCR Array is a 96-/384-well plate or 100-well disc that contains gene-specific Primer Assays for a thoroughly researched set of relevant, pathway- or disease-focused genes. It simultaneously profiles the expression of 84 pathway-specific genes, and five housekeeping genes. Each RT² Profiler PCR Array also includes a Genomic DNA Control (GDC) assay, triplicate Reverse Transcription Controls (RTC), and triplicate Positive PCR Controls (PPC).
FAQ ID -2718
What are the guidelines for choosing a housekeeping gene for normalizing qPCR results?

If you are unsure of the correct housekeeping gene(s), review the literature and technical information in your field to determine which gene(s) other researchers commonly use. It is recommended that multiple housekeeping genes be utilized for each gene expression experiment, to account for any impact that an experimental condition may have on the expression of an individual housekeeping gene. For a systematic assessment of which housekeeping genes are appropriate for your specific experimental conditions, we recommend using the Housekeeping Genes RT2 Profiler PCR Arrays for human (330231 PAHS-000), mouse (330231 PAMM-000), or rat (330231 PARN-000). These arrays consist of 8 sets of 12 common housekeeping genes. They are a valuable tool for easily identifying genes with a constant level of expression among your different experimental conditions.

FAQ ID -2674
How can I ensure that reaction volume is not lost due to evaporation during thermal cycling?
Be sure to carefully and completely seal the qPCR assay plate with fresh, optical, thin-wall, 8-cap strips or adhesive optical film before the plate is placed into the real-time cycler. In addition, refer to your instrument's user's manual to determine whether the real-time cycler manufacturer recommends use of a plate compression pad during the run.
FAQ ID -2679
Do you always run samples in triplicates?
No. Data Analysis can be done with a little as 2 PCR Arrays. Whether or not you run a sample in triplicate is determined by experimental setup and what you are going to use the data for.
FAQ ID -2703
Is it good to pool multiple RNA replicates to detect expression changes that are consistently reproducible?
With the additional RT2 PreAMP methodology, only 1 ng of RNA is now needed for PCR Array analysis. Pooling RNA from different sources should only be done when there is not enough sample. We recommend running biological replicates.
FAQ ID -2663
How do I create a workspace that is free of DNA contamination, prior to carrying out a qPCR experiment?

Any DNA contamination will artificially inflate the SYBR Green signal, yielding skewed gene expression profiles and false-positive signals. The most common source of DNA contamination is from PCR products generated during previous experiments. Such contamination is most often due to the improper disposal of tubes, tips, and gels that previously came into contact with PCR products. Additionally, PCR products may also contaminate pipettors, racks, work pads, and commonly used reagents such as water and buffers. To minimize the risk of contaminating your experiment with extraneous DNA, the following steps should be taken:

 

  • Remove a single aliquot of water from your PCR-grade stock, sufficient to complete the experiment. This minimizes the number of times that the stock container is opened, thereby minimizing contamination risks.
  • Use only fresh PCR-grade reagents and disposable labware.
  • Treat any labware (tubes, tips, and tip boxes) used in PCR with 10% bleach, before discarding.
  • Maintain a dedicated workspace for PCR setup (perhaps a PCR-only hood), away from areas of the lab where post-PCR work is done, such as running gels, enzyme digestions, and cloning.
  • Change the lab bench pads/papers often and decontaminate lab benches and labware (racks, pipettors, etc.) before each use by washing with 10% bleach, and/or exposing to UV light for at least 10 minutes. This serves to degrade and/or inactivate contaminating DNA.
  • Before, during, and after the experiment, minimize the opening and closing of any tubes or plates used during the experiment.  
FAQ ID -2654
On which instrumentation will the RT² Profiler PCR Array work?

For real-time detection, the RT² Profiler PCR Array is currently available for most QIAGEN, ABI, BioRad, Eppendorf, Stratagene, TaKaRa, Fluidigm, Cepheid, and Roche real-time instruments. Please refer to the link below, to determine which RT² Profiler PCR Array plate format is compatible with your instrument.

http://www.sabiosciences.com/manuals/PCRArrayGuide.pdf

FAQ ID -2719
What negative controls are typically included in qPCR and/or qRT-PCR experiments?

The 3 most common negative controls included in a qPCR and/or qRT-PCR experiment are as follows:

1. A no template control (NTC) omits any DNA or RNA template from a reaction, and serves as a general control for extraneous nucleic acid contamination. When using SYBR Green chemistry, this also serves as an important control for primer dimer formation. Within the RT2 Profiler PCR Arrays, the GDC well also serves as a no template control, as this assay is designed to detect Genomic DNA.

2. A no reverse transcriptase control (NRT) or minus reverse transcriptase control (MRT) involves carrying out the reverse transcription step of a qRT-PCR experiment in the absence of reverse transcriptase. This control assesses the amount of DNA contamination present in an RNA preparation.

3. A no amplification control (NAC) omits the DNA polymerase from the PCR reaction. This is a control for background fluorescence that is not a function of the PCR. Such fluorescence is typically attributable to the use of a degraded, dual-labeled probe. This control is unnecessary when utilizing SYBR-Green probe chemistries.

FAQ ID -2672
Do I need to run a standard curve before the actual PCR array experiment?
There is no need to run a standard curve before doing the RT2 PCR Array experiment. Usually we recommend starting with 1000 ng total RNA for a 96-well PCR array.
FAQ ID -2664
What are the most reliable methods for preparing high-quality RNA from cell or tissue samples, for use in gene expression analysis experiments?
We recommend the use of RNeasy Mini Kits. Cultured cells, and freshly isolated white blood cells, may be harvested by centrifugation, and used directly with this kit. For the isolation of high-quality RNA from animal tissues, we recommend RNeasy Plus Universal Kit.
FAQ ID -2657
What are the main differences between the qBiomarker PCR Arrays and the RT2 Profiler PCR Arrays?
The qBiomarker PCR Arrays contain gene lists that have been biologically validated and selected to measure the expression of a limited number of genes that are highly predictive for a biological process. Each qBiomarker PCR Array is designed to analyze multiple samples on the same 96-well or 384-well PCR plate. These arrays are best suited for screening and validation applications for a specific biological process. In contrast, the RT2 Profiler PCR Arrays typically have 84 pathway focused genes which are selected based on a different bioinformatic process and are best suited for gene expression profiling applications where a relative fold change result, and not a predictive answer, is necessary.
FAQ ID -2438
How can I predict the percent qPCR signal due to contaminating DNA, for a given qPCR assay, and its matching NRT control?

Assuming 100% amplification efficiency, each step increase in Ct value represents a doubling in the amount of qPCR template. Therefore, evaluating the difference in Ct values between the qPCR assay, and its matching NRT control, leads to the following predictions:

CtNRT - Ct+RT Fraction of gene expression signal due to contaminating DNA Percentage of gene expression signal due to contaminating DNA
1 (1/21) = 1/2 50%
2 (1/22) = 1/4 25%
3 (1/23) = 1/8 13%
4 (1/24) = 1/16 6%
5 (1/25) = 1/32 3%

FAQ ID -2688
How can I determine whether amplification occurs from mRNA-derived cDNA or from genomic DNA contamination?
The most rigorous method to detect genomic DNA contamination, particularly with the RT² qPCR Primer Assays, is to perform a No Reverse Transcriptase (NRT) control. The PCR will have no cDNA template derived from mRNA, and any detectable product could only have been derived from genomic DNA contamination.
FAQ ID -2687
Why are my qPCR Ct values too low (< 12) in my qRT-PCR Assay?
You may be using too much template. Use less input total RNA for reverse transcription, or use template at a greater dilution factor (lower concentration). Do not pipet a volume of less than 1 μl.
FAQ ID -2684
What is a dissociation curve, and why is it important to run a dissociation curve, following qPCR using SYBR Green chemistry?

Dissociation curves are carried out at the end of a PCR experiment by following a 3-step procedure.

First, all the components are denatured at 95°C, followed by complete annealing at a set temperature (based on the primer Tm values), followed by a gradual increase in temperature up to 95°C. Fluorescence intensity is monitored during this final temperature increase, resulting in the generation of a melting curve or dissociation curve.

By analyzing the first derivative of such a curve, you can readily assess the homogeneity of the PCR products, including the presence of primer–dimers, thereby determining the specificity of the PCR reaction. It is important to carry out such post-PCR analyses when using SYBR Green probe chemistry due to this reagent's lack of sequence specificity.

FAQ ID -2678
What positive controls are typically included in qPCR and/or qRT-PCR experiments?

It is critical to include appropriate positive controls in a qPCR experiment to determine if false negatives are being detected in the experiment. Positive controls fall into one of 2 classes.

1. Exogenous positive controls refer to the use of external DNA or RNA carrying a target of interest. If these positive controls are assayed in separate wells/tubes from the experimental sample, they serve as a control to determine whether or not the reverse transcription and/or PCR reaction conditions are optimal. Additionally, exogenous DNA or RNA positive controls may be spiked into the experimental sample(s), and assayed in parallel or in a multiplex format with, the target of interest. These control reactions assess whether the samples contain any components that inhibit reverse transcription and/or PCR.

2. Endogenous positive controls refer to the use of a native target that is present in the experimental sample(s) of interest, but is different from the target under study. These types of controls are often referred to as normalizers, and are typically used to correct for quantity and quality differences between samples.

Within the RT2 Profiler PCR Arrays, the Positive PCR Control (PPC) wells contain a plasmid with a primer assay that detects a sequence it produces. This allows for quick confirmation of the performance of the PCR steps.

The RTC wells include assays that detect the artificial RNA that is spiked in to each sample during the cDNA synthesis step. This ensures the Reverse Transcription step proceeded as needed.

FAQ ID -2673
Will the Reverse transcription control on the RT2 profiler PCR array work on any cDNA library?

The Reverse transcription control requires that the reverse transcription is done with the RT2 first strand kit. No other cDNA synthesis method can use this control. 

FAQ ID - 3534
Why is 18S ribosomal RNA (rRNA) used as a housekeeping gene to normalize sample-to-sample, systematic variation in qPCR assays?
18S ribosomal RNA is a widely used control for qRT-PCR analyses because of its invariant expression across tissues, cells, and experimental treatments. However, due to its extremely high expression in most cell types, it can sometimes be challenging to use 18S rRNA as an endogenous normalizer for several gene expression assays in the same reaction.
FAQ ID -2675
Can I manually set the threshold line?
You can manually set the threshold line. If you are using a catalogued PCR Array, the PPC values should be 20 +/- 2 Cts. Use the same threshold on all of your PCR Arrays.
FAQ ID -2702
What is the delta Rn value?
The Rn value, or normalized reporter value, is the fluorescent signal from SYBR Green normalized to (divided by) the signal of the passive reference dye for a given reaction. The delta Rn value is the Rn value of an experimental reaction minus the Rn value of the baseline signal generated by the instrument. This parameter reliably calculates the magnitude of the specific signal generated from a given set of PCR conditions. For more information, please refer to your cycler's user manual.
FAQ ID -2681
How do you determine the efficiency using the PCR array?
We determine the amplification efficiency during wet bench testing of our assays using standard curve dilutions, or by single curve analysis. If you would like to calculate the efficiency of each curve using single curve analysis, then you can try Real-Time PCR Miner, LinReg or Dart PCR. Each of these can be found using a GOOGLE search.
FAQ ID -2701
May I try the data analysis tool without using your PCR array kit?
Yes, all you need to do is to organize your data into a “custom PCR Array” file. When you upload it to the website, use the custom PCR array name CUSTOM. The locations of the blank excel spreadsheet is: http://www.sabiosciences.com/pcrarraydataanalysis.php#custom
FAQ ID -2698