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What type of assay did you use?
Did you select the right TaqMan Assay?
Applied Biosystems offers more than one million TaqMan® Gene Expression Assays. All assays have been designed with the Applied Biosystems validated bioinformatics pipeline and can be run with the same PCR protocol, eliminating the need for primer design or PCR optimization. However, it is important to select the correct assay for the transcript and RNA source. The Online Ordering Guide and the Online Selection Guide are documents that help you understand all the useful information on the Applied Biosystems homepage that supports the selection of the ideal assay for the intended research.
To ensure that your TaqMan® Gene Expression Assay does not contribute to failure of amplification, you may need to confirm the following information:
Reverse transcription (RT) is the process by which RNA is used as a template to synthesize cDNA. The single stranded cDNA molecule serves as a template for the real-time PCR. Different RT methods can have significant impact on real-time results. The RT reaction is often overlooked when troubleshooting late CT values (>35) or when no amplification is observed. Considerations have to be made for the type of RT reaction that was performed (one-step or two-step), the linearity of the RT reaction, and the range of RNA input (capacity) the RT chemistry will tolerate.
RNA that contains inhibitory compounds (e.g., sample preparation reagents, excessive protein) can lead to partial or complete inhibition of downstream PCR. PCR inhibitors originating from the starting material include heparin (>0.15mg/mL), proteins such as hemoglobin (>1mg/mL), polysaccharides, chlorophylls, melanin, and humic acids. Contaminants from the nucleic acid extraction phase include SDS (>0.01% w/v), phenol (>0.2% w/v), ethanol (>1%), proteinase K, guanidinium, and sodium acetate (>5mM).
How to identify PCR inhibition:
Analyze RNA samples with a UV spectrophotometer, bioanalyzer or Nanodrop to assess quantity and quality. A high quality RNA sample should have an A260/A280 UV spectrophotometer reading close to 2. It has been observed that an A260/A280 reading of 1.8 suggests there is about 70-80% of protein in the samples - there are many proteins that inhibit both PCR and reverse transcription.
Inhibition plot: You can use real-time PCR data from standard curve plots to determine whether inhibition is occurring at a level that causes spurious results. When used to characterize inhibition, these semi-log standard curves are referred to as inhibition plots. Please refer to the RNA Preparation and Reverse Transcription section of the Guide to Performing Relative Quantitation of Gene Expression Using Real-Time Quantitative PCR.
Solution
Possible causes of no amplification when using Custom TaqMan Gene Expression Assays include:
Your gene of interest may not be expressed at a high level in your sample type, or the sample types you extract from yield very low nucleic acid, e.g., obtained by cell sorting, LCM, or FFPE.
For guidance on how to assess the amount of RNA input for your real-time PCR study, refer to page 25 of the Guide to Performing Relative Quantitation of Gene Expression Using Real-Time Quantitative PCR.
Solutions:
Publication: Noutsias, M. et al. (2008) Preamplification techniques for real-time RT-PCR analyses of endomyocardial biopsies. BMC Mol Biol 9(1):3
Which transcript variants of your gene of interest are expressed in the particular tissue/cells used for RNA extraction?
To get more information about variants, do the following:
Once you get the results from your TaqMan® Gene Expression Assay search on the Assay Search results page, use the Alignment Map link to get an overview of all known transcripts for the gene of interest. Hyperlinks from the assay details page direct you to NCBI, where you can access more information about the gene of interest, such as mRNA sequence information, Gene ontology, and GEO (gene expression omnibus) profiles. If you are interested in detecting all transcript variants with your assay, make sure that you select an assay that detects all or most variants.
Use the GeneAssist™ siRNA Workflow Builder to simplify your search for the ideal assay. This collection of over 350 interactive cell signaling pathways gives you easy access to gene and disease information and enables you to order corresponding TaqMan® Gene Expression Assays and Ambion® Silencer® and Silencer® Select siRNAs. The GeneAssist™ Pathway Atlas provides you with lists of genes, proteins and products related to a particular pathway (e.g., BRCA1 pathway), visualized in over 350 interactive pathway maps. You can use the gene lists to configure your TaqMan® Array or TaqMan® Express Plate by exporting it for upload into the respective ordering tools.
For Research Use Only. Not for use in diagnostic procedures.