TaqMan™ Copy Number Reference Assay, human, RNase P
Beginning August 15, 2014, this product will ship under ambient conditions. Full details can be found here.
TaqMan™ Copy Number Reference Assay, human, RNase P
Applied Biosystems™

TaqMan™ Copy Number Reference Assay, human, RNase P

Green features
Human TaqMan™ Copy Number Reference Assays are run with human TaqMan™ Copy Number Assays in a duplex real-time PCR reactionRead more
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Catalog NumberNo. of Reactions
44033283000 Reactions
4403326750 Reactions
Catalog number 4403328
Price (USD)
525.65
Online Exclusive
564.00
Save 38.35 (7%)
3,000 reactions
Add to cart
No. of Reactions:
3000 Reactions
Price (USD)
525.65
Online Exclusive
564.00
Save 38.35 (7%)
3,000 reactions
Add to cart
Human TaqMan™ Copy Number Reference Assays are run with human TaqMan™ Copy Number Assays in a duplex real-time PCR reaction to detect and measure copy number variations (CNVs) and smaller regions in the human genome. Two options for genes that can be used as endogenous reference genes in humans are offered: RNase P and TERT. TaqMan™ Copy Number Reference Assays are designed to unique genomic sequences in the reference genome assembly (build GRCh38) and are required for relative quantitation of copy number targets.

TaqMan™ Copy Number Assays quantitate the gene of interest and normalize to an endogenous reference gene known to be present in two copies in a diploid genome. Please note that TaqMan™ Copy Number Reference Assays are species specific.

RNase P: The Standard Reference Gene Option
TaqMan™ Copy Number Reference Assays have a VIC™ dye–labeled TAMRA™ probe and reference sequence–specific forward and reverse primers. The assays are not primer-limited.

TaqMan™ Copy Number Reference Assay RNase P is recommended as the standard reference assay for copy number analysis. This assay detects the Ribonuclease P RNA component H1 (H1RNA) gene (RPPH1) on chromosome 14, cytoband 14q11.2. The assay location is chr.14:20343370 on build GRCh38. It has an 87 bp amplicon that maps within the single exon RPPH1 gene.

TaqMan™ Copy Number Reference Assay TERT is an alternative reference assay; it is recommended in the event that the RNase P assay functions poorly with a sample because of chromosomal aberrations or other issues. This assay targets the telomerase reverse transcriptase (TERT) gene located on chromosome 5, cytoband 5p15.33. The assay location is chr5:1253257 on build GRCh38. It has an 88 bp amplicon that maps within exon 16 of the TERT gene.

Simplest Copy Number Analysis Workflow
TaqMan™ Copy Number Assays have the simplest workflow of all currently available copy number analysis methods. The test assay (FAM™ dye–labeled), the reference assay (VIC™ dye–labeled), your sample DNA, and TaqMan™ Master Mix are combined and then run on an Applied Biosystems™ real-time PCR system using the standard TaqMan™ Copy Number Assay protocol. On average, setup to primary analysis takes only 3–4 hr (including an approximately 2 hour PCR run).

Powerful Data analysis Software
CopyCaller™ Software was developed specifically for TaqMan™ Copy Number Assay data analysis. This free, easy-to-use software utilizes a graphical interface that quickly calculates the possible copy numbers for a set of samples in a run. It also gives a confidence value for each copy number call, and has outlier functionality.
For Research Use Only. Not for use in diagnostic procedures.
Specifications
3'Primer ModificationNone
5'Primer ModificationNone
Concentration20X
FormatTube
Gene SymbolRPPH1
Green FeaturesSustainable packaging
Internal Probe ModificationTAMRA™ Quencher (3'), VIC™ (5')
No. of Reactions3000 Reactions
Product LineTaqMan™
Product TypeConfigurable Assay
Purification MethodHPLC
Purity or Quality GradeRNase-Free, DNase-Free
Quantity3,000 reactions
Shipping ConditionAmbient Temperature
SpeciesHuman
Sufficient For3000 Reactions
TargetRNase P
Detection MethodPrimer-probe
FormFrozen
GC-Rich PCR PerformanceLow
Label or DyeVIC
PCR MethodqPCR
Reaction SpeedStandard
Unit Size3,000 reactions
Contents & Storage
Control Primer-Probe Set(s)
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Frequently asked questions (FAQs)

Can I use the CopyCaller Software if I am using a non-Applied Biosystems Real-Time PCR instrument?

Yes, although the data will not be directly compatible. You can use the example files that install with the CopyCaller Software as a template to use with your data. You will have to copy/paste in the sample/target names and Ct values before importing into CopyCaller Software.

My data will not import into the CopyCaller Software. What could be wrong?

In the instrument software, make sure that you selected “Results” from the export options. The data need to be set up as duplex reactions as well. If you ran the copy number assay and the reference assay in separate wells, the data will not be in the correct format.

CopyCaller Software gave the error "XXX.txt is not a compatible file and cannot be added to the analysis. Verify that the file format is compatible with the software." What can I do now?

Check your export results with the instrument software. The data columns need to be in the following order: Well, Sample Name, Target Name, Task Reporter, Quencher, CT. If needed, rearrange the columns and export the data again for CopyCaller Software.

My results are different from what I expected when working with your Copy Number Variation Assay. Is there something wrong with the assay?

Check that the reference assay is performing consistently across all samples. Check the concentration of your samples and make sure they are normalized. We also recommend you to use several copy number assays targeting the same variation to validate the data.

What can I do if the copy number confidence values are very low?

Confidence values can be low for several reasons. Check your data for the following:

- Large variability in ΔCt values across the plate.
- Low number of replicates per sample (recommendation is for at least 4 replicates per sample).
- Sample copy number is high (> 3). You may want to use copy number bins instead for high copy numbers. Also keep in mind that CopyCaller Software is best for copy ranges of 1-5. If you have higher copy numbers, such as with transfections/transductions, it is best to use a standard curve.

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