PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification - PubMed (original) (raw)

. 2010 Jan;38(Database issue):D792-9.

doi: 10.1093/nar/gkp1005. Epub 2009 Nov 11.

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PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification

Athanasia Spandidos et al. Nucleic Acids Res. 2010 Jan.

Abstract

PrimerBank (http://pga.mgh.harvard.edu/primerbank/) is a public resource for the retrieval of human and mouse primer pairs for gene expression analysis by PCR and Quantitative PCR (QPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. There are several ways to search for primers for the gene(s) of interest, such as by: GenBank accession number, NCBI protein accession number, NCBI gene ID, PrimerBank ID, NCBI gene symbol or gene description (keyword). In all, 26,855 primer pairs covering most known mouse genes have been experimentally validated by QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed from the PrimerBank web site.

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Figures

Figure 1.

Figure 1.

PrimerBank search results for beta-actin primers. The primer search function can be found on the PrimerBank homepage. The database was searched for mouse beta-actin primer pairs by PrimerBank ID (6671509a1) and the search results obtained are shown here. The primer sequences, lengths, _T_ms, location of primers on the amplicon and expected amplicon size can be seen.

Figure 2.

Figure 2.

cDNA and amplicon sequence for beta-actin primers. The full cDNA and amplicon sequences as well as the highlighted location of primers on the amplicon are seen here and can be viewed from PrimerBank by clicking on the cDNA and amplicon sequence link found on the primer information web page (seen in Figure 1).

Figure 3.

Figure 3.

Experimental validation data for beta-actin primers. All experimental validation data are seen here and can be viewed from PrimerBank by clicking on the validation results links found on the primer information web page (seen in Figure 1) and on the cDNA and amplicon sequence web page (seen in Figure 2). The QPCR amplification plot, the dissociation curve and agarose gel data can be seen followed by the sequence obtained, which users can scroll through. A summary of the BLAST results obtained can be seen below the sequencing result. A BLAST tool can be seen below the BLAST results, which can be used to directly BLAST the sequence obtained against the NCBI database. Also, a feedback table can be seen, where users can provide information about their experimental data using the primers.

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