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TaqMan™ RNase P Assay, VIC™ dye/QSY™ probe (Applied Biosystems™)

The Applied Biosystems™ TaqMan™ RNase P Assay with VIC™ dye-labeled QSY™ probe provides a pre-formulated assay for quantitating human RNase P. This assay enables relative gene expression quantification in cDNA samples when used with other gene expression assays. It consists of a VIC dye-labeled QSY probe plus sequence-specific forward and reverse primers. The assay can be used for multiplex or singleplex PCR reactions. For an assay with ABY™ dye-labeled probe rather than VIC dye-labeled probe, see Cat. No. 4485714.

Benefits of this assay include:

• Eliminate assay design time using pre-designed primers and pre-designed VIC dye-labeled TaqMan probe
• Minimize experimental optimization time
• Use in conjunction with FAM™ dye-labeled predesigned gene expression assays

Save time in assay design, formulation, and testing by using the TaqMan RNase P Assay as your control when quantifying gene expression. This pre-designed probe and primer set enables you to normalize the amount of sample RNA or DNA in a reaction when used with a control sample. Or use it for relative gene expression quantification in cDNA samples when used with other gene expression assays.

The VIC dye is optimized for use with the second filter of our QuantStudio™, ViiA™ 7, and 7500 series real-time PCR instruments.

TaqMan™ MicroRNA Assay (Applied Biosystems™)

Applied Biosystems TaqMan MicroRNA Assays quantitate miRNAs with the specificity and sensitivity of TaqMan Assay chemistry. A simple, two-step protocol requires only reverse transcription with an miRNA-specific primer, followed by real-time PCR with TaqMan probes. TaqMan MicroRNA Assays are:

Highly specific—quantitate only mature miRNAs, not precursors
Sensitive—conserve limited samples, requires only 1–10 nanograms of total RNA or equivalent
Fast, simple and scalable—two-step quantitative RT-PCR assay provides high-quality results in less than three hours

Our TaqMan MicroRNA Assay catalogue is kept up to date with the Sanger database to provide comprehensive coverage with the most current annotation.

Availability and sizes
Made-to-Order assays are available in four different sizes and usually ship within two weeks. Inventoried assays are prepackaged in Small size and are ready to ship. Inventoried assays may be purchased in larger sizes by ordering them as Made to Order.

Species
TaqMan MicroRNA Assays are available for a range of species including human, mouse, rat, Drosophila, C. elegans, and Arabidopsis. We will continue to increase the number of miRNA assays for these species in alignment with the Sanger miRBase Registry.

Assay Components
TaqMan MicroRNA Assays are delivered in two tubes: one containing the RT primer, the other containing the specific pre-formulated TaqMan Assay (TaqMan probe and PCR primer set).

TaqMan miRNA Assay selection guide

 TaqMan MicroRNA AssaysTaqMan Advanced miRNA Assays
DescriptionTaqMan MicroRNA Assays employ a novel target-specific stem–loop primer during cDNA synthesis to produce a template for real-time PCRTaqMan Advanced miRNA Assays employ a universal RT step for a streamlined workflow, and a universal miR-Amp step to enable highly sensitive detection by real-time PCR
RT chemistrymiRNA-specific RTUniversal RT
ThroughputBest for 1–10 targetsBest for >10 targets
Coverage205 species available, coverage for miRBase v.21All human, mouse, and rat miRNAs; coverage for miRBase v.21

M13/pUC Reverse Sequencing Primer (-26), 17-mer (Thermo Scientific™)

Thermo Scientific M13/pUC sequencing primers anneal to the region in the 5'-terminus of the lacZ gene. All primers are supplied as 10 µM aqueous solutions.

Applications

• Sequencing of DNA fragments inserted into the MCS within the lacZ gene of various cloning vectors, such as pUC19, pTZ19R, pTZ57R, M13mp18, and pBluescript II
• Colony screening by PCR

Custom TaqMan™ Small RNA Assay (Applied Biosystems™)

Custom TaqMan Small RNA Assays use TaqMan Real-Time PCR Assays for the analysis of any small RNA molecule. The novel adaptations in TaqMan Assay design developed for the study of miRNAs are ideal for analysis of any small nucleic acid less than 200 bases long, including newly discovered miRNAs, Piwi-interacting RNA (piRNA), small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA).

Flexible and convenient ordering—easy process with our secure Custom TaqMan Small RNA Assay design tool
Versatile application—use for the analysis of any small RNA from any species
Reliable outcome—pre-formulated assays are optimized to run under universal conditions
Powerful miRNA quantitation—the same sensitivity, specificity, and reproducibility as predesigned TaqMan MicroRNA Assays

Sophisticated design pipeline
The miRPipe Small RNA Assay design pipeline is founded on our extensive background and bioinformatics expertise designing TaqMan Gene Expression Assays. To detect very small targets, it includes design features based on empirical data gathered over years of experiments. The resulting automated pipeline includes built-in flexibility features enabling design of assays for the broadest assortment of small RNA sequences. The benefits of TaqMan Assay technology are ideal for analysis of virtually any small RNA, enabling results you can trust from the very first experiment.

Ordering information
First, bioinformatically qualify your sequence target for specificity and sequence quality, then use the Custom TaqMan Small RNA Assay Design Tool to input your sequence and submit it for assay design. This easy-to-use tool is a secure and confidential. If we are unable to design or manufacture an assay for your sequence target of interest, you will not be charged.

M13 Forward (-20) (Invitrogen™)

Oligonucleotides complementary to a DNA template are necessary to prime DNA synthesis for sequencing reactions. Invitrogen offers a wide selection of single-strand primers that may be used in either single- or double-stranded sequencing protocols. All sequencing primers are non-phosphorylated and are supplied lyophilized.

All primers are:

Desalted and purified by gel filtration
• Assayed for function in automated sequencing reactions
• Supplied in quantity of 2 µg

TaqMan™ Gene Expression Assay, VIC primer-limited (Applied Biosystems™)

Applied Biosystems TaqMan Gene Expression Assays, VIC primer-limited, are used for quantitative real-time PCR analysis of gene expression and consist of a pair of unlabeled PCR primers and a TaqMan probe with a dye label (VIC) on the 5’ end and a minor groove binder (MGB) and nonfluorescent quencher (NFQ) on the 3’ end. These assays are primer-limited and ideal for multiplex reactions looking at two different gene targets in the same qPCR well.

Features include:
Easy to use—just add cDNA and master mix and run the qPCR—no melt curves required
Specific—TaqMan assays use proprietary MGB-containing probes that can be up to 15 bases shorter than non-MGB probes, improving the specificity of the assay
Sensitive—TaqMan assays are ideal for measuring low levels of expression or low-abundance targets
Accurate—identify small fold-changes with high accuracy of quantitation
Extensive content—over 1.8 million predesigned assays available for over 25 different species
Gold-standard TaqMan qPCR chemistry—TaqMan assays draw on Thermo Fisher Scientific's bioinformatics assay design pipeline to help ensure high specificity and minimal cross-reactivity, even for gene variants with high sequence homology
Ideal for multiplexing—combine one FAM-labeled and one VIC-labeled assay to create a duplex assay for two different gene targets in the same qPCR well
Ideal for control assays—use a VIC primer-limited assay for high-expressing endogenous control genes

Approximate ship time
Made to order: 4–6 days in North America, 6–10 days in Europe

TaqMan Gene Expression assays are the gold standard in real-time PCR gene expression studies, built on more than 20 years of experience. Each assay includes target primers and a sequence-specific probe optimized for the best functional performance. No additional design, optimization, or melt curve analysis is needed. Available in a wide variety of formats and species, new assay designs are constantly added to help meet your research needs. TaqMan assays have been cited in over 40,000 publications and are backed by more than 350 patents. All of our predesigned TaqMan Gene Expression assays are covered by the TaqMan Assays qPCR Guarantee.*

Recommended master mix: TaqMan Fast Advanced Master Mix

*Subject to terms and conditions. For complete details, go to www.thermofisher.com/taqmanguarantee.

Sequence Detection Primer (Applied Biosystems™)

Sequence detection primers are unlabeled primers that can be used with TaqMan probes or SYBR Green dye for your real-time PCR research applications.

Features include:
• Choice of delivered scales
• For use in any real-time PCR or PCR application
• All sequence detection primers are desalted

Real-time PCR sequence detection primers are delivered in either dry or liquid format.

Guaranteed yield
The unit size you select is based on the minimum amount we will deliver, not on synthesis starting amount.

Approximate ship time
4–6 days in North America, 5-10 days in Europe

We also offer:
• Custom TaqMan probes with a variety of options for dyes and quenchers. Learn more ›
• TaqMan MGB probes and primers available as predesigned and pre-formulated TaqMan Assays. Learn more ›
• Commercial manufacturing products and services, including OEM and GMP oligo manufacturing. Learn more ›

Need a different dye or concentration or a larger lot size? The TaqMan Custom Assay and Oligo Service offers custom products that you can tailor to meet your experimental needs. Learn more ›

M13/pUC Sequencing Primer (-40), 17-mer (Thermo Scientific™)

Thermo Scientific M13/pUC sequencing primers anneal to the region in the 5'-terminus of the lacZ gene. All primers are supplied as 10 µM aqueous solutions.

Applications

• Sequencing of DNA fragments inserted into the MCS within the lacZ gene of various cloning vectors, such as pUC19, pTZ19R, pTZ57R, M13mp18, and pBluescript II
• Colony screening by PCR

Custom TaqMan™ Gene Expression Assay, FAM (Applied Biosystems™)

Applied Biosystems Custom TaqMan Gene Expression assays are the custom version of our predesigned TaqMan assays for quantitative real-time PCR. The Custom TaqMan Gene Expression assays consist of a pair of unlabeled PCR primers and a TaqMan probe with a dye label (FAM) on the 5’ end and a minor groove binder (MGB) and nonfluorescent quencher (NFQ) on the 3’ end.

Features include:
Easy to use—just add cDNA and master mix and run the qPCR—no melt curves required
Specific—TaqMan assays use proprietary MGB-containing probes that can be up to 15 bases shorter than non-MGB probes, improving the specificity of the assay
Sensitive—TaqMan assays are ideal for measuring low levels of expression or low-abundance targets
Accurate—identify small fold-changes with high accuracy of quantitation
Gold-standard TaqMan qPCR chemistry—TaqMan assays draw on Thermo Fisher Scientific's bioinformatics assay design pipeline to help ensure high specificity and minimal cross-reactivity, even for gene variants with high sequence homology
Sequences provided with every Custom TaqMan Gene Expression Assay you design and order

Approximate ship time
Made to order: 4–6 days in North America, 6–10 days in Europe

TaqMan Gene Expression assays are the gold standard in real-time PCR gene expression studies, built on more than 20 years of experience. Each assay includes target primers and a sequence-specific probe optimized for the best functional performance. No additional design, optimization, or melt curve analysis is needed. Available in a wide variety of formats and species, new assay designs are constantly added to help meet your research needs. TaqMan assays have been cited in over 40,000 publications and are backed by more than 350 patents.

Recommended master mix: TaqMan Fast Advanced Master Mix

See also: Custom Plus TaqMan RNA Assays, designed using the full bioinformatic power of the TaqMan Assay design pipeline.

M13 Reverse (Invitrogen™)

Oligonucleotides complementary to a DNA template are necessary to prime DNA synthesis for sequencing reactions. Invitrogen offers a wide selection of single-strand primers that may be used in either single- or double-stranded sequencing protocols. All sequencing primers are non-phosphorylated and are supplied lyophilized.

All primers are:

Desalted and purified by gel filtration
• Assayed for function in automated sequencing reactions
• Supplied in quantity of 2 µg

TaqMan™ QSY Probe (Applied Biosystems™)

Applied Biosystems TaqMan QSY probes are dual-labeled probes used for real-time PCR. TaqMan QSY Probes are designed for optimal sensitivity and performance in multiplex qPCR experiments. Current users of dark quencher probes, such as Black Hole Quencher (BHQ™) probes, can design custom QSY probes without changing probe sequences.

All TaqMan QSY probes are HPLC-purified and verified by mass spectrometry to help ensure lot-to-lot reproducibility between batches. Thermo Fisher Scientific has been a leader in qPCR probe manufacturing for over 20 years, with expertise in probe synthesis in a facility that is certified to ISO 13485.

Features of TaqMan QSY probes include:
Sensitivity—lower background and increased signal result in better sensitivity
Multiplexing performance without compromise—successfully multiplex multiple gene targets in a single reaction
Dye options ideal for Applied Biosystems qPCR instrument filters—TaqMan qPCR dyes are designed for optimal alignment with Applied Biosystems qPCR instruments, enabling improved fluorescence signal, especially for low-expressing gene targets
Flexibility—mix and match your multiplex qPCR probes with up to two MGB probes or four QSY probes in a single reaction
Get started quickly—BHQ probe sequences can be converted to QSY versions with no redesign needed
Performance without compromise
Multiplexing with TaqMan QSY probes enables cost savings and preservation of limited samples, and has been shown to yield comparable results between reactions performed in individual tubes and in 4-plex reactions for gene quantification.

Learn more about multiplex real-time PCR ›

Guaranteed yield
The unit size you select is based on the minimum amount we will deliver, not on synthesis starting amount.

Approximate ship time
4–6 days in North America, 5-10 days in Europe

We also offer Applied Biosystems custom primers and other types of TaqMan probes. Learn more ›

Need a different dye or concentration or a larger lot size? The TaqMan Custom Assay and Oligo Service offers custom products that you can tailor to meet your experimental needs. Learn more ›

Megaplex™ Primer Pools, Rodent Pools B v3.0 (Applied Biosystems™)

Megaplex™ Primer Pools, Rodent Pool B v3.0 is available under a single part number containing both the Megaplex™ RT Primers and Megaplex™ PreAmp Primers, Rodent Pools B v3.0. Megaplex™ RT Primers, Rodent Pool B contains RT primers for 306 and 135 unique microRNAs for mouse and rat respectively plus 4 species specific controls. For use when assay sensitivity is of the utmost importance, Megaplex™ PreAmp Primers significantly enhance the ability to detect low expressed microRNAs enabling the generation of a comprehensive expression profile using far less sample, as low as 1 ng of input total RNA. The microRNA targets represented in this pool tend be less well characterized, more narrowly expressed and⁄or expressed at a lower level compared to Rodent Pool A. Rodent Pool B is intended for use with the TaqMan Rodent MicroRNA B Array v3.0, however, it can also be used to prepare cDNA for real-time analysis using the individual TaqMan® MicroRNA Assays.

Custom TaqMan™ Copy Number Assay (Applied Biosystems™)

Applied Biosystems TaqMan Copy Number Assays use gold-standard TaqMan MGB probe chemistry to evaluate the copy number of genomic DNA targets using Applied Biosystems real-time PCR instruments and software. TaqMan Copy Number Assays are run together with a TaqMan Copy Number Reference Assay in a duplex qPCR reaction; the copy number assay detects the target sequence, and the reference assay detects a sequence that is known to be present in two copies in the diploid genome. The results are then analyzed by the relative quantitation method using Applied Biosystems CopyCaller Software.

Custom TaqMan Copy Number Assays are an option for targets of interest that are not covered by the predesigned assay collection. The GeneAssist Copy Number Assay Tool enables you to submit your own premasked custom target sequences for assay design or primer/probe pair sequences for assay formulation, at no extra charge. The design process for Custom TaqMan Copy Number Assays does not include up-front bioinformatic sequence analysis or in silico QC, but the designs can be compared with the human/mouse reference assays for compatibility in duplex reactions.

Benefits:
Flexible—generate assays for any target of interest using the GeneAssist Copy Number Assay Tool, with no species limitations
Specific—gold standard TaqMan chemistry with minor groove binder (MGB) probes increase assay specificity by enabling shorter probes
Reproducible—robust assay designs developed with our optimized algorithms deliver accurate, reproducible, and reliable results
Easy to interpret—CopyCaller Software provides the calculated copy number and predicted copy number, along with confidence value and z-score quality metrics
Fast and simple—setup to primary analysis in 3–4 hours

Approximate delivery time
4–6 days in North America and 6–10 days in Europe

TaqMan Assays have been cited in over 40,000 publications and are backed by more than 350 patents.

TaqMan Copy Number Reference Assays are sold separately.

Recommended master mix (sold separately): TaqMan Genotyping Master Mix

TrueGuide™ tracrRNA (Invitrogen™)

Invitrogen TrueGuide Synthetic tracrRNA is a 72-bp gRNA scaffold that hybridizes with TrueGuide Synthetic crRNAs to form a gRNA complex that directs Cas9 nuclease to a specific editing site within the genome. The performance of this two-piece gRNA system is boosted by the addition of 2’O-methyl analogs and 3’ phosphorothioate internucleotide linkages. These modifications enhance editing efficiency by increasing binding to the target site and inhibiting nuclease degradation, respectively. The modifications are incorporated into the terminal three nucleotides on the 5’ and 3’ ends of both the TrueGuide Synthetic tracrRNA and the TrueGuide Synthetic crRNAs. TrueGuide Synthetic tracrRNA is available in three package sizes: 5 nmol, 20 nmol, and 100 nmol.

AgriSeq™ Canine Traits and Disorders Panel (Applied Biosystems™)

The Applied Biosystems AgriSeq Canine Traits and Disorders Panel contains 154 markers targeting clinically important canine traits and disorders. The panel includes SNPs and complex markers such as MNPs and InDels. Most of these markers are common to all breeds, while some are breed-specific for certain traits and conditions. The AgriSeq Canine Traits and Disorders Panel enables multiplexed simultaneous genotyping using the AgriSeq targeted genotyping-by-sequencing (GBS) workflow. The CanFam 3.1 reference genome is used for the analysis.

The need for highly consistent detection of informative genetic markers is critical for genetic trait detection. Targeted GBS methods, like AgriSeq, have the advantage over non-targeted GBS approaches (e.g., RADSeq) that are highly susceptible to allele drop-outs and missing data. Using the AgriSeq workflow, hundreds to thousands of markers can be targeted simultaneously in a highly reproducible manner across diverse sample sets. In collaboration with multiple experts and ISAG member laboratories, we have developed and validated the performance of all markers in the panel, including 97 SNPs, 6 MNPs, 13 insertions, and 38 deletions. The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse canine oral swab DNA samples. The comprehensive AgriSeq Canine Traits and Disorders Panel is designed to deliver reliable genotyping results for clinically important genetic disorders and traits.

Features of the AgriSeq Canine Traits and Disorders Panel include:
• Reproducible genotyping of 154 markers targeting 136 genetic disorders and 18 traits
• Simple, high-throughput workflow
• Customizable approach to combine with compatible parentage and identification markers

>99% mean sample call rate for markers
A high genotype call rate and reproducibility are imperative to accurately predict traits and disorders. Highly diverse canine oral swab DNA field samples were evaluated using the AgriSeq targeted GBS workflow, and a 99.5% mean sample call rate was obtained for a majority of the markers (see figure below). Replicate genotype concordance was >99.9% and calls were highly concordant with orthogonal data (>99%).

Simple, high throughput workflow
The AgriSeq Canine Traits and Disorders Panel has been optimized for use in the AgriSeq targeted GBS workflow. Up to 768 unique samples can be pooled per chip, greatly reducing the sequencing cost and labor per animal. Up to four 384-well plates can be processed in a single day and full sequencing results can be obtained in as little as three days. The flexibility of the AgriSeq workflow allows hundreds of samples to be pooled together into a single sequencing run targeting hundreds to thousands of markers.

Combine with Canine Parentage & Identification panel or customize panel with additional markers for maximal test value
The AgriSeq targeted GBS workflow is highly flexible, allowing the addition of compatible markers and panels for efficient, high-value genotyping. Whether you are looking to combine parentage analysis with specific desired trait markers or genetic defect markers to cull out carriers in breeding programs, our dedicated team of agrigenomics bioinformatics specialists is available to help design high performance panels.

The AgriSeq Canine Traits and Disorders panel, along with the AgriSeq workflow, provides a streamlined, cost-effective method for canine genotyping for traits and disorders.

NOTE: The CanFam 3.1 reference genome and other files needed for analysis of the AgriSeq Canine Traits and Disorder Panel can be obtained by contacting technical support.