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Resource:PrimerBank

Name: Resource:PrimerBank
Description: PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). 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: GenBank Accession, NCBI protein accession, NCBI Gene ID, Gene Symbol, PrimerBank ID or Keyword (gene description) or you can blast your gene sequence against the primerbank Sequence DB.

The primer design algorithm has been extensively tested by real-time PCR experiments for PCR specificity and efficiency. We have tested 26,855 primer pairs that correspond to 27,681 mouse genes by Real Time PCR followed by agarose gel electrophoresis and sequencing of the PCR products. The design success rate is 82.6% (22,187 successful primer pairs) based on agarose gel electrophoresis.

All experimental validation data for mouse primers are available from PrimerBank.

Polymerase Chain Reaction Amplification (PCR) is one of the most actively used techniques in molecular biology. In recent years, PCR has been increasingly used for gene expression detection or quantification. It is a more convenient method in gene expression studies comparing to other techniques, such as Northern Blot. One common problem in PCR is the non-specific amplifications of other gene products because cDNAs libraries of thousand of genes are often used as PCR templates.

Therefore, we need to carefully design PCR primers that specifically amplify the genes of interest. Unfortunately, most available primer design programs only focus on primer chemical properties, such as melting temperature, GC content, secondary structure, etc. Little emphasis is given to primer mispriming to other genes. In contrast, all primers in PrimerBank were carefully designed to ensure gene specificity.

You can submit your primers. We will add your primers to our database once they are properly QCd.[1]
Other Name(s): PrimerBank: PCR Primers for Gene Expression Detection and Quantification
Parent Organization: Harvard Medical School; Massachusetts; USA
Supporting Agency: NIH
Resource Type(s): Web accessible database, Data storage repository
Keywords: electrophoresis, expression, gc content, gel, gene, agarose, algorithm, amplification, human, molecular probe, primer database, mouse, PCR, primer, primer pair, protein, quantification, reaction, secondary structure, Polymerase Chain Reaction, Real-time
Grant: U01 HL66678
Abbreviation: PrimerBank
Resource: Resource
URL: http://pga.mgh.harvard.edu/primerbank/
PMID: PMID 19906719, 19108745, 14654707
Publication link: http://nar.oxfordjournals.org/content/38/suppl_1/D792.full
Id: nif-0000-21333
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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References

  1. Spandidos A et al. (2010) PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification. Nucleic Acids Res 38: D792-9 PubMed

Notes

This page uses this default form:Resource

Contributors

Aarnaud, Ccdbuser, Nifbot2



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Facts about Resource:PrimerBankRDF feed
AbbrevPrimerBank  +
CurationStatuscurated  +
DefiningCitationhttp://pga.mgh.harvard.edu/primerbank/  +
DefinitionPrimerBank is a public resource for PCR pr PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). 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: GenBank Accession, NCBI protein accession, NCBI Gene ID, Gene Symbol, PrimerBank ID or Keyword (gene description) or you can blast your gene sequence against the primerbank Sequence DB.

The primer design algorithm has been extensively tested by real-time PCR experiments for PCR specificity and efficiency. We have tested 26,855 primer pairs that correspond to 27,681 mouse genes by Real Time PCR followed by agarose gel electrophoresis and sequencing of the PCR products. The design success rate is 82.6% (22,187 successful primer pairs) based on agarose gel electrophoresis.

All experimental validation data for mouse primers are available from PrimerBank.

Polymerase Chain Reaction Amplification (PCR) is one of the most actively used techniques in molecular biology. In recent years, PCR has been increasingly used for gene expression detection or quantification. It is a more convenient method in gene expression studies comparing to other techniques, such as Northern Blot. One common problem in PCR is the non-specific amplifications of other gene products because cDNAs libraries of thousand of genes are often used as PCR templates.

Therefore, we need to carefully design PCR primers that specifically amplify the genes of interest. Unfortunately, most available primer design programs only focus on primer chemical properties, such as melting temperature, GC content, secondary structure, etc. Little emphasis is given to primer mispriming to other genes. In contrast, all primers in PrimerBank were carefully designed to ensure gene specificity.

You can submit your primers. We will add your primers to our database once they are properly QCd.
o our database once they are properly QCd.
ExampleImagePrimerBank.PNG  +
GrantCategory:U01 HL66678   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleWeb accessible database  +, and Data storage repository  +
Idnif-0000-21333  +
Is part ofHarvard Medical School; Massachusetts; USA  +
KeywordsElectrophoresis  +, Expression  +, Gc content  +, Gel  +, Gene  +, Agarose  +, Algorithm  +, Amplification  +, Human  +, Molecular probe  +, Primer database  +, Mouse  +, PCR  +, Primer  +, Primer pair  +, Protein  +, Quantification  +, Reaction  +, Secondary structure  +, Polymerase Chain Reaction  +, and Real-time  +
LabelResource:PrimerBank  +
ModifiedDate14 November 2011  +
PMID19906719, 19108745, 14654707  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://nar.oxfordjournals.org/content/38/suppl_1/D792.full  +
SuperCategoryResource  +
Supporting AgencyNIH  +
SynonymPrimerBank: PCR Primers for Gene Expression Detection and Quantification  +