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?
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
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)?
What type of control RNA is included in the TaqMan® Rodent GAPDH kit (P/N 4308313)?
Are there any TaqMan® Endogenous Controls reagents available that can be used with rat samples?
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
Do the human and rodent GAPDH primers and TaqMan® probe sequences manufactured by Applied Biosystems® detect genomic DNA?
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
In the TaqMan® Rodent GAPDH Control Reagents kit (P/N 4308313), what rodent is the Control RNA isolated from?
Do your human and rodent GAPDH primers and TaqMan® probe sequences detect genomic DNA?
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