What is the context sequence for a TaqMan™ Gene Expression Assay?

Product FAQ

Answer

The context sequence is 25 nucleotides that includes the probe sequence. The context sequence is available only after the purchase of an assay and is provided in the AIF (Assay Information File) that comes on the CD with the order shipment.

Answer Id: E1995

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5b39ccdd3321ba462c10382541e5cd2f_FAQ

Why can't I find a TaqMan™ Gene Expression Assays for a particular target of interest?

Product FAQ

Answer

There are two reasons an assay won't be found on the website: 1) an assay does not yet exist for the transcript of interest, or 2) the search criteria were insufficient.

It is easiest to search for an assay using a RefSeq ID, hCG, or hCT. If searching by gene symbols, it is best to omit hyphens, dashes, etc. Also, it is recommended to limit the number of characters to 3 and append an asterisk (*), which is the wildcard search symbol. If an assay is not found using RefSeq IDs, it should be assumed that the assay is currently in the design/manufacturing pipeline and will be available on the web in the near future. High homology within certain gene families can slow the design process because it is harder to make gene-specific assays. If you do not find your particular gene expression assay, you can order a Custom TaqMan™ Gene Expression Assay. For more information, review the "Custom TaqMan™ Assays -Design and Order Guide".

Answer Id: E1996

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92c41ccf7151e7bedffcc71f45dd5405_FAQ

Why are there are two TaqMan™ Gene Expression Assays for the same gene. Are these the same assay?

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Answer

It is possible that there is more than one assay for a particular gene, but they are designed across different locations on the gene. Information on where the assay is located and which RefSeqs/GenBank entries are detected can be found on the Assay Details Page. It is also possible that there are two assays for the same gene that are designed on the same location. When there are multiple options, we recommend to choose the "Best Coverage" assay (based on its selection criteria).

Answer Id: E1997

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ddbb45253b3b105eec5ddfe5ded8c3b0_FAQ

A TaqMan™ Gene Expression Assay that has been used in the past is no longer on the website. Why?

Product FAQ

Answer

Content associated with each assay is gathered from a variety of public and private sources. These sources are continuously being updated. In an effort to keep our data current, we perform in silico QC of the assay and its associated content approximately every 6 months. This automated process may prohibit an individual assay from being displayed on the web at a given time.

Answer Id: E1998

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a4ea5ee00cdd27436a46942a4d0897d7_FAQ

I am getting positive signals for the no template controls (NTCs) in one TaqMan™ Gene Expression Assay, but not in any others. Is it possible that the assay was contaminated during manufacturing?

Product FAQ

Answer

This is very unlikely, as an NTC test is performed for every round of assay manufacture. Any assay failing this test is thrown out and re-synthesized and tested. Only assays passing all of our QC tests are put into inventory and are available for sale.

Answer Id: E1999

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1e36601ea966410e3936889251a81e98_FAQ

Do you functionally test all the TaqMan™ Gene Expression Assays?

Product FAQ

Answer

We do not functionally test all TaqMan™ Gene Expression Assays. However, a statistically significant number of human, mouse, and rat assays have been functionally tested. The same assay development pipeline was used for all Gene Expression assays customized for the specific genome. The informatics pipeline includes extensive in silico QC, ensuring specificity and reproducibility.

Answer Id: E2000

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d4b4da0222a44be4db67be0350a0ec31_FAQ

Do you test the TaqMan™ Gene Expression Assays for PCR efficiency?

Product FAQ

Answer

Several hundred TaqMan™ Gene Expression Assays have been tested for PCR efficiency. When tested across a 6-log range, all assays approached 100% efficiency (+/- 10%). This statistically significant number of tested assays validates the design pipeline. For more information on the efficiencies of TaqMan™ Gene Expression Assays please consult the Application Note entitled "Amplification Efficiency of TaqMan™ Assays-on-Demand Gene Expression Products"

Answer Id: E2001

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d28914631f8b5c52f1210ae25eb40fc2_FAQ

What is the NCBI Reference Sequence (RefSeq) listed with an TaqMan™ Gene Expression Assays, and how can I get more information on the NCBI Reference Sequence (RefSeq) project?

Product FAQ

Answer

The NCBI Reference Sequence project (RefSeq) provides reference sequence standards for the naturally occurring molecules. The NCBI RefSeq project maintains the current knowledge of sequence information and the corresponding biology, and avoids the redundancy often present in the GenBank database archive.

Answer Id: E2003

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bcc7eeee941db424ca9fa9064b679d70_FAQ

Are the TaqMan™ Gene Expression Assays (P/N 4331182) designed to detect genomic DNA?

Product FAQ

Answer

No, genomic DNA is not a intended template of these assays, but some of them may detect it along with cDNA depending on their design. For multi-exon genes, which are denoted with "m1" at the end of the Assay ID, the assays are designed to amplify target cDNA without amplifying any genomic DNA. Assays denoted with "s1" at the end of the Assay ID, are designed within an exon (usually because the gene only has one exon) and by definition, will detect genomic DNA. Assays denoted with "g1" at the end of the Assay ID, are designed across an exon-exon junction and may detect genomic DNA, because the intron is very small

Answer Id: E2004

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9dfa32d66911f1017ce494a7fa3c26ff_FAQ

What are the advantages of using the TaqMan™ Gene Expression Assays (P/N 4331182)?

Product FAQ

Answer

The TaqMan™ Gene Expression Assays accelerate human disease research studies by providing quantitative gene expression assays for all human genes. They are an essential tool for screening more array hits faster and easier. The assays utilize the 5' nuclease chemistry, which provides maximum sensitivity with a wide dynamic range. This allows for standardization of gene expression data resulting in direct data comparison between labs.

Answer Id: E2005

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a4800cf615e802c312d3df71a22a1cdc_FAQ

Are the primers that are included in the TaqMan™ Gene Expression Assays limited?

Product FAQ

Answer

The primers that are included are at non-limiting concentrations. This means that the TaqMan™ Gene Expression Assays are not designed to be used in a multiplex assay.

Answer Id: E2006

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c396126893cf77dfcbb6460750a04dce_FAQ

Can I use SYBR® Green I dye in conjunction with the TaqMan™ Gene Expression Assays or Custom TaqMan™ Gene Expression Assays?

Product FAQ

Answer

No, SYBR® Green dye I is not compatible with the TaqMan™ Gene Expression Assays or Custom TaqMan™ Gene Expression Assays. Gene Expression Assays or Custom TaqMan™ Gene Expression Assays contain TaqMan™ MGB probes combined with primers at non-limiting concentrations. The probes already have detection dyes conjugated to them, and SYBR® Green is not needed. For more information, please consult the protocol of TaqMan™ Gene Expression Assays and Custom TaqMan™ Gene Expression Assays.

Answer Id: E2007

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b58e43e753475ba9a5091b2b49f424f0_FAQ

What are the storage conditions for the TaqMan™ and Custom TaqMan™ Gene Expression and SNP Genotyping Assays?

Product FAQ

Answer

After shipment, the assay mixes should be stored at -15 C to -20 C to maximize stability. Freeze/thaws should be kept to a minimum (a maximum of 10 freeze-thaw cycles is recommended). Keep all TaqMan™ and Custom TaqMan™ Gene Expression and SNP Genotyping Assays protected from direct exposure to light. Excessive exposure to light may affect the fluorescent probes. If desired, the Assay Mix may be diluted with TE buffer or DNase-free Water. It is recommended to make working stocks from the stock solutions provided in these kits.

Answer Id: E2008

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01c012371f770f15ec1d25e0ec8aebcd_FAQ

When preparing the RNA for the TaqMan™ Gene Expression Assays or Custom TaqMan™ Gene Expression Assays, is it necessary to denature the RNA sample?

Product FAQ

Answer

No, it is not always necessary to denature the RNA. Denaturation of the RNA may reduce the yield of cDNA for some gene targets. For more information, please consult the TaqMan™ Gene Expression Assays or Custom TaqMan™Gene Expression Assays protocols.

Answer Id: E2011

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2f0d282451fc64241b9e809472f40135_FAQ

How much cDNA is recommended per TaqMan™ or Custom TaqMan™ Gene Expression reaction?

Product FAQ

Answer

For optimal performance of the TaqMan™ and Custom TaqMan™ Gene Expression Assays, use 1 to 100 ng of cDNA per 50 ul total reaction volume. For more information, please consult the TaqMan™ Gene Expression Assay protocol and Custom TaqMan™ Gene Expression Assay protocol.

Answer Id: E2012

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e56924eb60d44a090765c944bc0e9373_FAQ