This document provides information about TaqMan Gene Expression Assay products from Applied Biosystems. It offers pre-designed probe and primer sets (TaqMan Gene Expression Assays) for quantifying gene expression in common model organisms like human, mouse, rat, Arabidopsis, and Drosophila. It also describes options for custom assays with user-designed sequences. The assays use TaqMan chemistry and real-time PCR for sensitive and reproducible gene expression analysis.

1. Product Guide TaqMan® Gene Expression Assay Products
TaqMan Gene Expression Assays
®
Product Guide

2. Applied Biosystems TaqMan ®
Gene Expression Assays Solutions
Applied Biosystems offers the largest family of products to meet your quantitative
gene expression needs: from off-the-shelf gene-specific probe and primer sets to
Custom TaqMan® probes and primers manufactured to your desired sequences,
and everything in between. All products use TaqMan® probe-based chemistry and
are designed for use on the suite of Applied Biosystems Real-Time PCR Systems—
together the gold standard in quantitative gene expression offering the greatest
sensitivity, specificity, reproducibility, and the broadest dynamic range.
Table of Contents
TaqMan® Gene Expression Assays 2
Custom TaqMan® Gene Expression Assays 4
TaqMan® Endogenous Controls 5
TaqMan® Low Density Array 7
Custom TaqMan® Probes and Primers 9
TaqMan® MicroRNA Assays 10
Applied Biosystems Real-Time PCR Systems 12
Product Specification Comparison Back Cover
Which TaqMan® TaqMan® Custom TaqMan® TaqMan® Custom TaqMan®
Gene Expression Product Gene Expression Assays Gene Expression Endogenous Probes and
Is Right for You? Inventoried Non-Inventoried Assays Controls Primers
Convenience of fully-formulated
assay (premixed probe and primers)
No specific preference on
assay location within a gene
Specific location within
a transcript is key
FAM™ dye label
is fine
Need a specific
reporter dye label
Prefer to use an
Applied Biosystems design
Prefer to use my own
sequence target
Prefer to design my own
probe and primers
Non-universal
probe-primer concentration
pg. 1 | www.appliedbiosystems.com

3. TaqMan® Gene Human Assays strains. By avoiding areas in the gene
Expression Assays Over 100,000 gene expression assays transcripts of known polymorphisms,
• Gene-specific TaqMan® probe are available for all known human we design only strain-neutral gene
and primer sets for quantitative genes. These include genes in the expression assays.
gene expression studies in human, public domain with associated RefSeq
mouse, rat, Arabidopsis, and transcripts (NCBI Reference Sequence Arabidopsis and Drosophila Assays
Drosophila species project database: http://www.ncbi. Over 130,000 assays have been
nlm.nih.gov/RefSeq), the mammalian designed for most known genes for
• Convenient single-tube format
gene collection (MGC), and GenBank® Arabidopsis thaliana and Drosophila
• Universal cycling conditions melanogaster. Similar to the assays for
database. A minimum of one assay
(probe and primer set) per RefSeq other species, these assays have been
TaqMan® Gene Expression Assays
transcript is available as an inventoried, designed against the public RefSeq
are a comprehensive collection of
off-the-shelf product currently num- database. The collection includes assays
over 600,000 pre-designed probe and
bering 21,000 assays. The complete for nearly every known transcript for
primer sets that let researchers quickly
collection includes assays for nearly each organism, and all assays are
and easily perform quantitative gene
every exon junction in all known available on a made-to-order basis.
expression studies on human, mouse,
rat, Arabidopsis, or Drosophila genes. human genes in the public domain Comprehensive Coverage
Each gene expression assay consists of covering most probes on the Applied and Selection
a FAM™ dye-labeled TaqMan® MGB Biosystems Expression Array System. Not only have we designed an assay
probe and two PCR primers formu- for every gene, but also for multiple
Mouse and Rat Assays
lated into a single tube. Every assay locations across each gene transcript.
Over 200,000 mouse and rat assays
is optimized to run under universal More than 600,000 high-quality assay
have been designed for all known genes.
thermal cycling conditions with a final designs are available for human, mouse,
As with our human assays, at least one
reaction concentration of 250 nM rat, Arabidopsis, and Drosophila genes
assay per RefSeq transcript has been
for the probe and 900 nM for each on a made-to-order basis. This vast
manufactured and is available from our
primer. This streamlined approach and selection allows researchers to select the
inventory. High quality assay designs
comprehensive assay selection enables specific location on a given transcript
for all other genes are also available
a convenient, standardized process they wish to detect. For instance,
on a made-to-order basis, as
for quantitative gene expression. microarray researchers that may prefer
non-inventoried assays.
a 3' bias in their TaqMan® probe and
Strain-Neutral Mouse and Rat Assays primer sets will be able to select from
The assay design process yields strain- robust, pre-designed TaqMan® Gene
neutral mouse and rat gene expression Expression Assays. Additionally,
assays. Polymorphisms are the cause researchers performing RNAi studies
of most sequence variability between can choose multiple assays per gene
to validate their knockdown results.
TaqMan® Gene Expression Assays are delivered with a compact disc containing an electronic assay information file.
www.appliedbiosystems.com | pg. 2

4. State-of-the-Art Assay
Design Bioinformatics
All assays are designed using Applied
Biosystems sophisticated bioinformatics
pipeline, customized for either the
human, mouse, rat, Arabidopsis, or
Drosophila genome. This pipeline
consists of three main steps:
Step One
Both public and Celera sequence data are
used to identify the optimal probe and
primer locations. This process consists of:
• Mapping transcripts to the genome
to identify exon boundaries
• Masking sequence discrepancies
between public and Celera data
• Masking sequence repeats The Applied Biosystems online catalog map view graphically represents the assay’s physical location on the gene, and
which transcript(s) each assay detects.
• Masking known SNPs from both
public and Celera databases
catalog and are available on a made-to- to each of the eight sample ports and
Step Two order basis. Our graphical map viewer run on an Applied Biosystems 7900HT
Proprietary software algorithms shows each assay’s location on the Fast Real-Time PCR System. For more
generate probe and primer designs for gene, to help determine which assay information, see the “TaqMan® Low
the locations identified above. These is most appropriate. Density Array” section on page 7.
algorithms include optimal design
Choice of Delivery Formats A TaqMan® Genomic Assay Catalog
parameters, such as %GC content, Tm,
Applied Biosystems delivers the assays CD is also available. This off-line version
amplicon length, and low secondary
in either a tube-format or TaqMan® Low of our catalog allows you to search and
structure, to ensure high amplification
Density Array-format (using inventoried select our assays without an Internet
efficiency. Where possible, designs span
assays only). The TaqMan® Low Density connection. Download a version today
an exon-exon junction, eliminating the
Array is a 384-well micro fluidic card at www.allgenes.com or request a copy
possibility of detecting genomic DNA.
that streamlines reaction set-up time, from your sales representative.
Step Three eliminates the need for liquid handling
Convenient Assay Ordering Options
In silico QC ensures each assay is robotics, and provides standardization
Both our online catalog and CD
specific to the gene for which it across multiple users and/or multiple
catalog enable searching for your
was designed (i.e., the assay will not labs. This format is ideal for analyzing
target of interest by:
detect sequences from other genes, many samples across a fixed number of
or pseudo-genes). Each assay design targets, such as for biomarker screening. • Gene name
is processed through a quality scoring The TaqMan® Array arrives ready to • Accession number
system and one high scoring, gene- use, with your selected TaqMan® Gene (NCBI RefSeq ID number, etc.)
specific assay design is sent to our Expression Assays preloaded into each of
• Gene family, or functional categories
state-of-the-art manufacturing facility. the 384 reaction wells. Simply add 100
and groups (kinase, transcription
All designs meeting our scoring criteria µL sample mix (sample cDNA and
factor, ion channel, cytokine, etc.)
are also displayed in our online TaqMan® Universal PCR Master Mix)
pg. 3 | www.appliedbiosystems.com

5. Custom TaqMan® Gene
Expression Assays
• Any species or organism
• Target sequence of your choice
• Convenient single-tube format
Custom TaqMan® Gene Expression
Assays are available for any species,
any splice variant, or any novel gene.
Simply download our free File Builder
Software to format and submit your
target sequence. File Builder Software
can be downloaded from our Web site
(http://home.appliedbiosystems.
com/support/software/filebuilder).
The software easily guides you through
the ordering process from selecting
the assay size, formatting your target
sequence to identify the location of
the probe, and submitting your order
via e-mail.
Custom TaqMan® Gene Expression Assays are delivered ready-to-use, along with the probe and primer sequences
you designed.
File submissions are done in a secure
format. Your target sequences and
the associated assays that are designed 96-position rack designed to accommo- into a single 20X mix. Designed to run
are kept confidential. With Custom date standard liquid handling robotics under universal conditions for two-step
TaqMan® Gene Expression Assays, and fit seamlessly into automated, high- RT-PCR, TaqMan® Gene Expression
you benefit from Applied Biosystems throughput laboratory processes. Each Assays are simple to use. Just add
proprietary software algorithms for order of assays also includes a compact TaqMan® Universal PCR Master Mix
probe and primer design, which enable disc with an assay information file that (with or without AmpErase® UNG)
you to obtain optimal assays for each includes the assay ID numbers, detector and your cDNA sample to generate
target sequence. Assays are delivered in names, reporter dye, and quencher sensitive, reproducible, and truly
a single-tube, ready-to-use format, along information for easy uploading into quantitative gene expression data
with the probe and primer sequences a LIMS or sequence detection on any Applied Biosystems Real-Time
designed from your submitted sequence. system software. PCR System.
Automation-Compatible to Accelerate A Simple, Standardized Solution Compared to do-it-yourself methods,
High-Throughput Applications for Quantitative Gene Expression TaqMan® Gene Expression Assays and
Both TaqMan® Gene Expression Assays TaqMan® Gene Expression Assays and Custom TaqMan® Gene Expression
and Custom TaqMan® Gene Expression Custom TaqMan® Gene Expression Assays eliminate weeks or even months
Assays come pre-formulated in a single, Assays are built on our 5' nuclease of probe and primer design, formula-
2D-barcoded tube with an easy-to-read chemistry and consist of a FAM™ tion, and testing.
label. The single-tube format requires dye-labeled TaqMan® MGB probe
For more information on this product,
fewer set-up and pipetting steps to (250 nM, final concentration), and
visit www.allgenes.com or check
assemble reactions, allowing you to two unlabeled PCR primers (900 nM
with your local Applied Biosystems
easily scale your throughput. Assay each, final concentration). All compo-
representative.
tubes are shipped in a 1D-barcoded nents are QC tested and formulated
www.appliedbiosystems.com | pg. 4

6. A Simple, Standardized Solution Choosing the Right
for Quantitative Gene Expression Endogenous Control
Each endogenous control is built Endogenous controls can normalize
on our 5' nuclease chemistry and is the expression levels of target genes by
offered in a choice of two different correcting differences in the amount
reporter dyes and two quenchers: of cDNA that is loaded into PCR reac-
• A FAM™ dye-labeled TaqMan® MGB tion wells. For best results, verify that
probe (250 nM, final concentration) the endogenous control is consistently
and two unlabeled PCR primers expressed in the sample set to be tested.
(900 nM each) Endogenous control expression must be
uniform across all samples in the study.
• A VIC® dye-labeled TaqMan® MGB For multiplexing, ensure that the gene
probe (250 nM, final concentration)
Each endogenous control is built on our 5' nuclease
expression level of the endogenous con-
and two unlabeled PCR primers
chemistry and is available in a number of reporter trol is greater than that of the target.
dye/quencher formats. (150 nM each—primer limited)
• A VIC® dye-labeled TAMRA™ Multiplex vs. Singleplex PCR
TaqMan® Endogenous Controls
dye-labeled probe (250 nM, final All TaqMan® Endogenous Controls
• Optimized, pre-formulated, concentration) and two unlabeled that contain probes labeled with the
ready-to-use control assays PCR primers (150 nM each— VIC® reporter dye are primer limited.
• Cost-effective gene expression primer limited) This allows multiplexing of TaqMan®
quantitation in human, mouse, Endogenous Controls with target
rat, Arabidopsis, Drosophila, All components are QC tested, gene expression assays, provided that
and eukaryotes formulated into a single 20X mix, and the control gene is more abundantly
functionally tested. Designed to run expressed than the target gene. All
• Choice of FAM™ or VIC® dye labels under universal conditions for two-step TaqMan® Endogenous Controls that
Applied Biosystems TaqMan® RT-PCR, our TaqMan® Endogenous contain probes labeled with the FAM™
Endogenous Controls are a collection Controls are simple to use. Just add reporter dye are not primer limited
of pre-designed probe and primer TaqMan® Universal PCR Master Mix and are not intended for multiplexing.
sets that can be used to normalize (with or without AmpErase® UNG)
and your cDNA sample to generate Complementary Products
the amount of sample RNA or DNA
sensitive, reproducible, and truly TaqMan® Endogenous Controls are
added to a reaction. For the quantita-
quantitative gene expression data intended to be used with:
tion of gene expression, deciding upon
a specific control can be difficult, even on ABI PRISM® 7000 and 7700 • TaqMan® Gene Expression Assays
when detailed information about the Sequence Detection Systems, • Custom TaqMan® Gene Expression
biological system is available. This Applied Biosystems 7300 and 7500 Assays
can result in trial and error to identify Real-Time PCR Systems, and Applied
• Custom TaqMan® Probes and Primers
an appropriate control, leading to Biosystems 7500 and 7900HT Fast
project delays and increased costs. Real-Time PCR Systems. Compared Online Ordering
Applied Biosystems offers endogenous to do-it-yourself methods, our Order from our line of TaqMan®
controls for the most commonly used TaqMan® Endogenous Controls Endogenous Controls through the
control genes in human, mouse, rat, deliver a complete quantitation Applied Biosystems store at
Arabidopsis, Drosophila, and any solution and eliminate weeks or http://store.appliedbiosystems.com
eukaryotic species. The assays are even months of assay design,
formulation, and testing. For more information on this product,
designed to let researchers quickly
check with your local representative or
and easily identify and run the best
visit www.allgenes.com
possible endogenous control for
their gene expression study.
pg. 5 | www.appliedbiosystems.com

7. TaqMan® Endogenous Controls
Number of
Dye/Quencher Part Number Primer Limited Conc. Reactions, 20 µL
Eukaryotic 18S rRNA VIC®/MGB 4319413E Y 20X 2,500
VIC /TAMRA
® ™
4310893E Y 20X 2,500
FAM™/MGB 4333760T N 20X 125
FAM™/MGB 4333760f N 20X 500
Human ACTB (beta actin) VIC®/MGB 4326315E Y 20X 2,500
VIC®/TAMRA™ 4310881E Y 20X 2,500
FAM /MGB
™
4333762T N 20X 125
FAM™/MGB 4333762F N 20X 500
Human B2M (beta-2-microglobulin) VIC®/MGB 4326319E Y 20X 2,500
VIC®/TAMRA™ 4310886E Y 20X 2,500
FAM™/MGB 4333766T N 20X 125
FAM /MGB
™
4333766F N 20X 500
Human GAPD (GAPDH) VIC®/MGB 4326317E Y 20X 2,500
VIC®/TAMRA™ 4310884E Y 20X 2,500
FAM /MGB
™
4333764T N 20X 125
FAM™/MGB 4333764F N 20X 500
Human GUSB (beta glucuronidase) VIC /MGB
®
4326320E Y 20X 2,500
VIC®/TAMRA™ 4310888E Y 20X 2,500
FAM™/MGB 4333767T N 20X 125
FAM /MGB
™
4333767F N 20X 500
Human HPRT1 VIC®/MGB 4326321E Y 20X 2,500
VIC®/TAMRA™ 4310890E Y 20X 2,500
FAM™/MGB 4333768T N 20X 125
FAM™/MGB 4333768F N 20X 500
Human PGK1 (phosphoglyceratekinase 1) VIC /MGB
®
4326318E Y 20X 2,500
VIC®/TAMRA™ 4310885E Y 20X 2,500
FAM /MGB
™
4333765T N 20X 125
FAM™/MGB 4333765F N 20X 500
Human PPIA (cyclophilin A) VIC®/MGB 4326316E Y 20X 2,500
VIC®/TAMRA™ 4310883E Y 20X 2,500
FAM™/MGB 4333763T N 20X 125
FAM /MGB
™
4333763F N 20X 500
Human RPLO (large ribosomal protein) VIC®/MGB 4326314E Y 20X 2,500
VIC®/TAMRA™ 4310879E Y 20X 2,500
FAM /MGB
™
4333761T N 20X 125
FAM™/MGB 4333761F N 20X 500
Human TBP (TATA-box binding protein) VIC /MGB
®
4326322E Y 20X 2,500
VIC®/TAMRA™ 4310891E Y 20X 2,500
FAM™/MGB 4333769T N 20X 125
FAM /MGB
™
4333769F N 20X 500
Human TFRC (CD71) (transferring receptor) VIC®/MGB 4326323E Y 20X 2,500
VIC®/TAMRA™ 4310892E Y 20X 2,500
FAM™/MGB 4333770T N 20X 125
FAM™/MGB 4333770F N 20X 500
Mouse GAPD (GAPDH) VIC /MGB
®
4352339E Y 20X 2,500
Mouse ACTB (beta actin) VIC®/MGB 4352341E Y 20X 2,500
Rat GAPD (GAPDH) VIC /MGB
®
4352338E Y 20X 2,500
Rat ACTB (beta actin) VIC®/MGB 4352340E Y 20X 2,500
Table 1.
www.appliedbiosystems.com | pg. 6

8. TaqMan® Low Density Array assays to run on the TaqMan® Array researchers in the field. All assays are
• TaqMan® performance in a low (for selection, visit www.allgenes.com). designed to genes with known implica-
density array format TaqMan® Arrays are available in nine tions in immune response. For conven-
• Micro fluidic technology provides different formats, covering 12, 16, 24, ience, these TaqMan® Array Immune
access to 384-well format without 32, 48, 64, 96 (2 choices), and 384 Panels are available in packs of ten.
liquid-handling robotics assays per array (Table 3). TaqMan®
Arrays are designed for use on the The endogenous control panel allows
• Standardization enables screening flexible Applied Biosystems 7900HT researchers to quickly identify the opti-
of multiple samples against selected Fast Real-Time PCR System. mal gene(s) to use as endogenous con-
gene panels trols for each gene expression study.
Ideal Screening Technology Eleven TaqMan® Endogenous Controls
The TaqMan® Low Density Array TaqMan® Low Density Arrays are ideal for human, plus five additional TaqMan
is an easy-to-use micro fluidic card for screening applications such as: Gene Expression Assays (identified
for real-time PCR. The micro fluidic as exhibiting minimal variation in
technology utilizes eight sample-loading • Biomarker screens
gene expression across sixteen human
ports, each connected to 48 reaction • Toxicology screens tissues), are pre-loaded in the TaqMan®
chambers, streamlining the reaction • Target class screens Array in triplicate. Eight samples can
set-up process and eliminating the be run on each array. The TaqMan®
need for liquid-handling robotics. • Pathway analysis
Array Endogenous Control Panels
Simply load 100 µL of sample mix, • Disease set analysis are available in packs of two.
(30 –100 ng of cDNA sample and
50 µL of 2X TaqMan® Universal PCR In addition to Custom TaqMan Arrays, Applied Biosystems 7900HT
Master Mix), into each of the sample Applied Biosystems also offers two Fast Real-Time PCR System
loading ports. Centrifuge briefly, seal versions of TaqMan® Low Density The TaqMan Array was designed
the TaqMan® Array, and run on the Array Panels—the TaqMan® Low expressly for the Applied Biosystems
Applied Biosystems 7900HT Fast Density Array Immune Panel and 7900HT Fast Real-Time PCR System,
Real-Time PCR System. the TaqMan® Low Density Array a flexible, high-throughput, Real-Time
Endogenous Control Panel. The PCR system that detects and quanti-
TaqMan® Low Density Arrays immune panel contains 96 TaqMan tates nucleic acid sequences. The
are delivered with your choice of Gene Expression Assays pre-loaded in combination of the TaqMan Array
inventoried TaqMan® Gene Expression quadruplicate across the 384 reaction and the 7900HT system helps make
Assays pre-loaded into each of the 384 wells. The assays were selected in high-throughput gene expression
reaction wells. Select from our collec- collaboration with the Immune research successful and easy.
tion of more than 40,000 inventoried Tolerance Network, as well as other
TaqMan® Low Density Array # of Samples per Card Minimum Order
Description # of Assays 1 Replicate 2 Replicates 3 Replicates 4 Replicates Quantities Part Number
Format 12 11 + 1 control 8 20 4342247
Format 16 15 + 1 control 8 20 4346798
Format 24 23 + 1 control 8 4 20 4342249
Format 32 31 + 1 control 4 20 4346799
Format 48 47 + 1 control 4 2 20 4342253
Format 64 63 + 1 control 2 20 4346800
Format 96a 95 + 1 control 2 1 20 4342259
Format 96b 95 + 1 control 2 1 20 4342261
Format 384 380 + 1 control 1 50 4342265
Immune Panel 96 2 1 10 4342510
Endogenous Control Panel 16 8 2 4367563
7900HT TaqMan Low Density Array Upgrade*
®
4329012
Includes: sample block, micro fluidic card sealer, custom buckets and adaptors, Getting Started guide, and chemical installation kit.
*A compatible centrifuge is required but not supplied.
Table 2.
pg. 7 | www.appliedbiosystems.com

9. Available TaqMan® Low Density Array Formats
Format 12 (part number 4342247) Format 64 (part number 4346800)
Format 16 (part number 4346798) Format 96a (part number 4342259)
Format 24 (part number 4342249) Format 96b (part number 4342261)
Format 32 (part number 4346799) Format 384 (part number 4342265)
Format 48 (part number 4342253)
Table 3. TaqMan® Low Density Arrays can be ordered in any one of these nine formats.
www.appliedbiosystems.com | pg. 8

10. Custom TaqMan® Probes will have a greater destabilizing effect Primer Express® Design Software
and Primers on an MGB probe, resulting in better Applied Biosystems Primer Express®
• Choice of dye labels, quenchers, discrimination. The shorter length also software is available to simplify the
and synthesis scales offers greater design flexibility for all probe and primer design process.
• Available for any species or organism real-time PCR applications. Primer Express® is available for
individual users and in multi-user
• For use in quantitative gene Applied Biosystems offers the tradi-
packs. Please check our Web site at
expression, SNP genotyping, other tional dual-labeled Custom TaqMan®
www.appliedbiosystems.com for
allelic discrimination applications, Probes with a TAMRA™ dye fluores-
more details.
and pathogen detection cent quencher as well. All TAMRA™
dye TaqMan® probes are HPLC And, if you prefer the convenience
When you know the exact sequences
purified. of a pre-designed probe and primer
you need for your TaqMan® Probes
set, check our vast online selection
and Primers, Applied Biosystems can A Selection of Reporter Dyes
of TaqMan® Gene Expression and
synthesize them for you. As the market Applied Biosystems Custom TaqMan®
SNP Genotyping Assays.
leader in real-time PCR, our high- Probes can be ordered with a variety
quality custom products can be used of different reporter dyes to facilitate Other Fluorescent Dye-Labeled
in all of your real-time and end-point your multiplexing applications. Oligos
PCR applications. These products offer Applied Biosystems also offers a
you the ideal in flexibility, whether you Synthesis Scales
host of other custom oligo products
prefer to optimize your own reaction TaqMan® Custom Probes and Primers
for use in many applications,
formulation, or if you simply want are available in a choice of three standard
including microsatellite-based linkage
to buy in large quantities. sizes. Each includes a pre-defined quan-
mapping, mutation detection, and
tity of probe or primer to ensure that
Our Custom TaqMan® Probes and more. Please see our Web site,
you get the same amount each time you
Primers are manufactured at three sites www.appliedbiosystems.com
order and aren’t subject to variations in
around the world—the United States, for more details.
synthesis yield. For larger synthesis scales
the United Kingdom, and Japan, to on these products, please contact your
offer excellent delivery time. Order by Applied Biosystems Sales Representative.
fax, e-mail, or online, and send your
sequences to our synthesizers electroni-
cally, speeding order delivery time. Probe Type (3' Quencher) 5' Reporter Dyes Probe Lengths
TaqMan® Custom MGB Probes FAM™ VIC® TET™, or NED™*
, , 13-25 bases
Choice of Quenchers
TaqMan® Custom TAMRA™ Dye Probes FAM™ VIC® or TET™
, , Up to 35 bases
Applied Biosystems Custom TaqMan®
Probes incorporate a 5' reporter dye Table 4.
and a 3' quencher. Our most popular *Please note that NED™ dye can give lower signal intensity than FAM™, VIC®, or TET™ dye on most Real-Time PCR systems.
The Applied Biosystems 7500 Real-Time PCR System has been optimized to yield higher signal intensity for NED™ dye.
quencher is a non-fluorescent quencher
(NFQ) combined with an MGB (minor
groove binder) moiety. The NFQ offers Custom TaqMan® Reporter
Probes and Primers Part Number Dye Label Quantity
the advantage of lower background
TaqMan® TAMRA™ Probes 450025 6-FAM™, VIC® or TET™ 6,000 pmol
signal, which results in better precision
450024 6-FAM , VIC or TET
™ ® ™
20,000 pmol
in quantitation. The MGB moiety
450003 6-FAM™, VIC® or TET™ 50,000 pmol
stabilizes the hybridized probe and
effectively raises the melting temperature TaqMan MGB Probes
®
4316034 6-FAM , VIC , NED or TET
™ ® ™ ™
6,000 pmol
(Tm). This means that MGB probes 4316033 6-FAM , VIC , NED or TET
™ ® ™ ™
20,000 pmol
can be shorter than traditional dual- 4316032 6-FAM™, VIC®, NED™ or TET™ 50,000 pmol
labeled probes, which make them better Real-Time PCR Primers 4304970 No label 10,000 pmol
(sequence detection primers)
suited for allelic discrimination applica- 4304971 No label 80,000 pmol
tions. The shorter probe lengths mean 4304972 No label 130,000 pmol
that single base mismatches (e.g., SNPs) Table 5.
pg. 9 | www.appliedbiosystems.com

11. TaqMan® MicroRNA Assays
• Highly specific—quantitate only
mature miRNAs, not inactive
precursors
A B
• Fast, simple, and scalable—two-step
assay provides high-quality results in
less than three hours
• Sensitive—conserves limited samples
by requiring only 1–10 nanograms of
total RNA or equivalent
• Wide dynamic range—up to
seven logs
By making novel adaptations in
Unparalleled dynamic range. Amplification plot of synthetic miRNA lin-4 by stem-loop RT-PCR. Estimated synthetic
assay design, Applied Biosystems is now miRNA input is based on OD: 70, 700, 7,000, 70,000, 700,000, 7M, and 70M copies in PCR. Significant correlation
able to bring the specificity, sensitivity, between the copy number and CT value up to seven orders of magnitude. A) amplification plot, B) amplification plot
converted to log scale.
and simplicity of TaqMan® assays and
Real-Time PCR to miRNA detection
and quantitation. conventional design of a random- Requires Only Minimal
primed RT step followed by a specific Starting Material
The basis of TaqMan® MicroRNA real-time assay. The stem-loop accom- TaqMan miRNA assays are extremely
Assays is a target-specific stem-loop, plishes two goals: 1) specificity for sensitive—researchers need only 1–10
reverse-transcriptase primer. Its only the mature miRNA target, and nanograms of purified total RNA or
innovative design (below) overcomes 2) formation of a RT primer/mature equivalent to reliably quantify their
a fundamental problem in miRNA miRNA-chimera, extending the 5' end miRNAs of interest, not the several
quantitation: the short length of of the miRNA. The resulting longer RT micrograms typically required for
mature miRNAs (~22 nt) prohibits amplicon presents a template amenable hybridization-based methods. Such
to Real-Time TaqMan assay design sensitivity enables researchers to
with great specificity. conduct more extensive experiments
looped RT primer with limited starting material, as with
mature microRNA To ensure accurate results, every
full-panel miRNA expression profiling.
individual TaqMan MicroRNA Assay
It also conserves researcher’s precious
design has been functionally validated
Step 1:
or difficult-to-obtain materials, such as
Stem-loop under laboratory conditions.
RT stem cells or matched tumor/normal
Distinguish Between Highly human cancer samples.
Homologous Mature miRNAs
Unparalleled Dynamic Range
TaqMan® miRNA assays are not only
Step 2:
TaqMan miRNA assays can deliver
Real-time specific for mature miRNAs, they can up to seven logs of linear dynamic
PCR
also successfully distinguish between range, from a few copies, to millions
forward primer highly homologous targets, and in some of copies (data above). This means
cases, with only a single nucleotide mis- that researchers will get accurate data
match. This means that researchers can whether their materials contain few
be confident that they are measuring or many molecules of the target
Q F reverse primer mature, biologically relevant miRNAs,
TaqMan® probe
miRNA per cell—an important
not precursors, and that closely related factor given the wide range of miRNA
TaqMan® MicroRNA Assay mechanism. A simple, miRNA variants have been targeted
two-step mechanism brings the advantages of
concentrations across different cells,
with very high specificity.
Real-Time PCR to miRNA quantification. tissue types, and disease states.
www.appliedbiosystems.com | pg. 10

12. This increased accuracy also makes Cost-Effective The kit supplies sufficient materials to
TaqMan miRNA assays highly repro- With a cost-per-target comparable perform 20 reactions (20 µL volume)
ducible among replicates and when to microarray experiments, TaqMan of each assay—enough for several
performed by different researchers. MicroRNA Assays are a powerful full-panel miRNA screens.
alternative. Not only are they conven-
Fast Time-to-Results ient and adaptable to high-throughput Because many mature miRNA
By taking advantage of gold-standard protocols, they also offer the superior sequences are identical across closely
TaqMan® reagent-based technology specificity, sensitivity, and dynamic related species, the majority of assays
with universal thermal cycling range of Real-Time PCR. in the Human Panel Kit are also
conditions, TaqMan miRNA assays valid for mouse and rat targets.
are familiar, fast, and easy to set up. Case Study: Comparison A cross-species chart detailing the
Just start with your total RNA sample, to Northern Analysis human, mouse, and rat microRNAs
and get results in less than three Recent studies showed that northern targeted by each individual assay
hours using any Applied Biosystems analysis and TaqMan MicroRNA Assay can be downloaded from the Web at
Real-Time PCR System. results correlated when both methods mirna.appliedbiosystems.com
were performed under ideal conditions.
A Convenient and Scalable Solution However, TaqMan miRNA assays are a 2. TaqMan® MicroRNA Assay
TaqMan miRNA assays are pre- better choice because: ABM 000008 hsa-miR-16
designed, functionally validated, and This is an individually available assay
available off-the-shelf from Applied • They can offer a high level of targeting the mature human miRNA
Biosystems, making them extremely discrimination between highly miR-16. The assay allows customers
convenient. Spend your valuable time homologous miRNA variants to easily evaluate TaqMan MicroRNA
generating results, not designing and • They are easy to use and provide Assay technology without having to
troubleshooting assays. results within three hours invest in the full human panel kit.
• They are highly sensitive, requiring Identified as a candidate positive
The TaqMan miRNA assay format is
minimal starting materials control for human miRNA quantifica-
easily amenable to high-throughput
tion experiments, miR-16 exhibits a
screening methods. All of the up to 157 • They have a dynamic range of
high level of expression across most
individual miRNA assays and controls up to seven logs
tissue types. Also, because the mature
contained in the Human Panel – Early
Early Access Product Availability miR-16 sequence is identical between
Access Kit fit into two 96-well plates.
Applied Biosystems has released the human, mouse, and rat, it is also useful
For example, a statistically rigorous
following two early access miRNA for quantifying the mouse and rat
experiment profiling the entire assay
products: miR-16 miRNAs.
panel in quadruplicate, including
multiple control assays, can be run 1. TaqMan® MicroRNA Assays Additional TaqMan MicroRNA
in just two 384-well plates. Human Panel – Early Access Kit Assay products will become
This product includes 157 individual available in the near future. Register
The Human Panel Kit provides miRNA assays and three non-human for product updates on the Web at
flexibility—researchers can run the negative control assays. The panel mirna.appliedbiosystems.com
entire panel together, or any subset covers the majority of human
of assays they wish. This scalable miRNAs currently identified
solution accommodates both large in the Sanger miRNA Registry
initial miRNA panel screens, and (http://microrna.sanger.ac.uk).
further in-depth experiments.
www.appliedbiosystems.com | pg. 11

13. Applied Biosystems 7900HT Fast Real-Time PCR System Applied Biosystems 7500HT Fast Real-Time PCR System
Applied Biosystems 500–660 nm, provides unmatched dye • Relative Quantitation Software allows
Real-Time PCR Systems resolution capabilities gene expression data from up to ten
Applied Biosystems Real-Time PCR • Automation Accessory provides walk plates to be combined in one analysis
Systems make real-time PCR more away automation for unmatched
accessible than ever before by providing Applied Biosystems 7300 Real-Time
throughput PCR System—an economical solution
powerful solutions to fit the needs of
any laboratory. These systems are easy to • Enterprise Edition Software enables setting the standard for the basic
use with next generation software, and hundreds to thousands of plates to be researcher
of course, they’re backed by Applied analyzed simultaneously and assists • Four color detection provides
Biosystems unmatched track record of with 21CFR part 11 compliance the flexibility to perform all
performance, quality, and long-term major applications
Applied Biosystems 7500 Fast and
reliability. 7500 Real-Time PCR Systems— • Powerful and versatile software
versatile platforms for users requiring makes experimental set-up and data
Applied Biosystems 7900HT Fast processing simple and straightforward
Real-Time PCR System—the ultimate extended capabilities
in performance and flexibility • Advanced five color optical config- • Precision optics and a charge-
• User-interchangeable block options uration supports a broader range of coupled device (CCD) camera
include 384-well, 96-well, TaqMan® fluorophores, with variable excitation provide highly accurate,
Low Density Array, and Fast 96-well capability allowing greater sensitivity reproducible, and reliable results
(for results in about 35 minutes) for longer wavelength (red) dyes • Patented sample temperature control
• Extended-life 488 nm argon-ion • A new high-speed 96-well thermal provides superior reproducibility and
laser combined with continuous cycling block enables real-time PCR consistent, high-quality results
wavelength detection from results in under 40 minutes
pg. 12 | www.appliedbiosystems.com

14. Product Specification Comparison
Available
Number of Reporter Universal Approximate
Part Number Fill Volumes 20 µL Reactions Dye Labels Formulation Delivery Time
TaqMan® Gene Expression Assays
Inventoried 4331182 250 µL, 20X 250 FAM™ Yes 2 – 3 days
Non-Inventoried 4351372 360 µL, 20X 360 FAM ™
Yes 10 – 14 days
Custom TaqMan® Gene 4331348 360 µL, 20X 360 FAM™ Yes 10 – 14 days
Expression Assays 4332078 750 µL, 20X 750 FAM ™
Yes 10 – 14 days
4332079 967 µL, 60X 2,900 FAM™ Yes 10 – 14 days
TaqMan Endogenous Controls
®
Primer limited Various — see Table 1 VIC® Yes
Not primer limited Various — see Table 1 FAM™ Yes
Custom TaqMan Probes
®
Various — see Table 5 FAM ™
No 4 – 7 days
Various — see Table 5 VIC® No 4 – 7 days
Various — see Table 5 TET ™
No 4 – 7 days
Various — see Table 5 NED ™
No 4 – 7 days
Available
Fill Volumes Number of Reporter Universal Approximate
Part Number (each assay) Reactions Dye Labels Formulation Delivery Time
TaqMan® MicroRNA Assays
(Early Access Products)
Human Panel Kit 4365409 RT: 60 µL, 5X; Up to 3,680 FAM™ Yes 2 – 3 days
(Includes 157 human 15 µL rxn vol. • 157 individual
miRNA assays, and miRNA assays
additional non-human (20 rxn each)
control assays, for a total TaqMan® Assay: • Additional
of up to 3,680 reactions) 40 µL, 10X; negative
20 µL rxn vol. control assays
(20 rxn each)
Individual hsa-miR-16 assay 4365746 RT: 450 µL, 5X 150 FAM™ Yes 2 – 3 days
(Targets human, mouse, 15 µL rxn vol.
and rat miR-16)
TaqMan® Assay:
300 µL, 10X;
20 µL rxn vol.
Reaction Number of Available Approximate
Part Number Size 1 µL Reactions Assays Delivery Time
Custom TaqMan® Low Density Arrays Various — see Table 2 1 µL 384 Any Inventoried TaqMan 6 – 8 weeks
Gene Expression Assay
TaqMan® Low Density Array Panels Various — see Table 2 1 µL 384 Defined Panels of TaqMan 2 – 3 days
Gene Expression Assays
Table 6.
For Research Use Only. Not for use in diagnostic procedures.
NOTICE TO PURCHASER:
PLEASE REFER TO THE USER’S GUIDE, PRODUCT INSERT, OR APPLIED BIOSYSTEMS’ PRODUCT PAGE FOR LIMITED LABEL LICENSE OR DISCLAIMER INFORMATION.
ABI PRISM, Applied Biosystems, Primer Express, and VIC are registered trademarks and AB (Design), Applera, Celera, FAM, NED, TAMRA, and TET are trademarks of Applera
Corporation or its subsidiaries in the US and/or certain other countries.
TaqMan and AmpErase are registered trademarks of Roche Molecular Systems, Inc.
©2005 Applied Biosystems. All rights reserved.
Printed in the USA, 09/05, Publication 127GU01-03
Headquarters International Sales
850 Lincoln Centre Drive | Foster City, CA 94404 USA For our office locations please call the division
Phone 650.638.5800 | Toll Free 800.345.5224 headquarters or refer to our Web site at
www.appliedbiosystems.com www.appliedbiosystems.com/about/offices.cfm