Since the TaqMan® Rodent GAPDH Control Reagents (Cat. No. 4308313) will also amplify pseudogenes and/or genomic DNA, is there some equation that can be used to correct for genomic DNA contamination?

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There is no equation for the correction of data for genomic contamination; however, a rule of thumb is that if the Ct difference between your target and the contaminant is 10 or more, you can assume it is not having an effect in your reaction. Please consult the TaqMan® Rodent GAPDH Control Reagents Protocol for more information on these reagents. Enter the catalog number in the main Search field on our web site to view the product detail page and the Protocol.

Answer Id: 1572

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452bf208bf901322968557227b8f6efe_FAQ

What is the GenBank accession number of the sequence that was used to design the primers and probe for the TaqMan® Rodent GAPDH Control Reagent Kit (P/N 4308313)?

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The GenBank accession number used is NM_008084. For more information on this kit, please refer to the TaqMan® Rodent GAPDH kit protocol.

Answer Id: 1811

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09b15d48a1514d8209b192a8b8f34e48_FAQ

What type of control RNA is included in the TaqMan® Rodent GAPDH kit (P/N 4308313)?

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The RNA included in the TaqMan® Rodent GAPDH kit is total RNA extracted from P388D1 lymphoma mouse cell line.

Answer Id: 1812

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5b6ba13f79129a74a3e819b78e36b922_FAQ

Are there any TaqMan® Endogenous Controls reagents available that can be used with rat samples?

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Answer

We have TaqMan® Endogenous Controls for 18S Ribosomal RNA and a kit (Cat. No. 4308313) that can be used with rat samples. The Eukaryotic 18S Ribosomal RNA Reagent is in a highly conserved area that allows this TaqMan® Endogenous Control to be used for rat, human and mouse. In addition, we have newer TaqMan® Gene Expression Rat Endogenous Controls, including beta glucuronidase and beta-2 microglobulin. These can be found by searching our Gene Expression Assays and specifying the species of interest as R. norvegicus and the set membership as Endogenous Controls.

Answer Id: 1006

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9246444d94f081e3549803b928260f56_FAQ

Do the human and rodent GAPDH primers and TaqMan® probe sequences manufactured by Applied Biosystems® detect genomic DNA?

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This depends on the individual probe. Potential reaction with genomic DNA - based on position of primers and/or probe within or across exon junctions - is one of the specifications indicated in the Assay search tool and product support materials. Here are details on the reported performance of a few specific products:

- Taqman® GAPDH Control Reagents, human, 402869, JOE™: Does not detect genomic DNA
- Taqman® Endogenous Control, GAPDH for human, 4326317E, VIC® : Does not detect genomic DNA
- Taqman® Endogenous Control, GAPDH, human, 4310884E, VIC®: Does not detect genomic DNA
- Taqman® Endogenous Control, GAPDH, human, 4333764F, FAM™: Does not detect genomic DNA
- Taqman® Endogenous Control, GAPDH, human, 4333764T, FAM™: Does not detect genomic DNA
- Taqman® Gene Expression Assay, GAPDH, human, Hs99999905_m1/4331182, FAM™: Does not detect genomic DNA

Answer Id: 1517

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81c8727c62e800be708dbf37c4695dff_FAQ

In the TaqMan® Rodent GAPDH Control Reagents kit (P/N 4308313), what rodent is the Control RNA isolated from?

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The control RNA is total RNA isolated from a mouse lymphoma cell line.

Answer Id: 1128

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3fe78a8acf5fda99de95303940a2420c_FAQ

Do your human and rodent GAPDH primers and TaqMan® probe sequences detect genomic DNA?

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It varies by product, so be sure to check all the available product specifications before purchase. Here are details on a few options:

- The TaqMan® GAPDH Control Reagents (Human), Cat. No. 402869, which is labeled with JOE™ dye, spans two exons therefore will not amplify genomic DNA.

- The Human GAPD (GAPDH) Endogenous Control (VIC®/ TAMRA™ Probe, Primer Limited), Cat. No. 4310884E, is also designed across an exon-exon boundary and will not amplify genomic DNA.

- The probe in the TaqMan® Rodent GAPDH Control Reagents kit, Cat. No. 4308313, labeled with VIC® dye, does not span an intron and therefore may amplify genomic DNA.

Answer Id: 1435

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