QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-12

AUTHORS

Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Riaño-Pachón, Bernd Mueller-Roeber

ABSTRACT

BACKGROUND: Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. RESULTS: Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%. CONCLUSION: QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays. More... »

PAGES

465

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-9-465

DOI

http://dx.doi.org/10.1186/1471-2105-9-465

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1024450931

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18976492


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Primers", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Internet", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleic Acid Probes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sensitivity and Specificity", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "User-Computer Interface", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Potsdam", 
          "id": "https://www.grid.ac/institutes/grid.11348.3f", 
          "name": [
            "Max-Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam-Golm, Germany", 
            "Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Stra\u00dfe 24-25, Haus 20, 14476, Potsdam-Golm, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Arvidsson", 
        "givenName": "Samuel", 
        "id": "sg:person.0764644363.16", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764644363.16"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Silesia", 
          "id": "https://www.grid.ac/institutes/grid.11866.38", 
          "name": [
            "Max-Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam-Golm, Germany", 
            "Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Stra\u00dfe 24-25, Haus 20, 14476, Potsdam-Golm, Germany", 
            "Department of Genetics, University of Silesia, Jagiellonska 28, 40032, Katowice, Poland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kwasniewski", 
        "givenName": "Miroslaw", 
        "id": "sg:person.01073755136.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073755136.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Potsdam", 
          "id": "https://www.grid.ac/institutes/grid.11348.3f", 
          "name": [
            "Max-Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam-Golm, Germany", 
            "Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Stra\u00dfe 24-25, Haus 20, 14476, Potsdam-Golm, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ria\u00f1o-Pach\u00f3n", 
        "givenName": "Diego Mauricio", 
        "id": "sg:person.01307302416.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01307302416.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Potsdam", 
          "id": "https://www.grid.ac/institutes/grid.11348.3f", 
          "name": [
            "Max-Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam-Golm, Germany", 
            "Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Stra\u00dfe 24-25, Haus 20, 14476, Potsdam-Golm, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mueller-Roeber", 
        "givenName": "Bernd", 
        "id": "sg:person.01355415616.67", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355415616.67"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1093/nar/gkm306", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003651676"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.108.088336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003655378"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.108.088336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003655378"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm999", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004115570"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2004-5-5-p11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004632209", 
          "https://doi.org/10.1186/gb-2004-5-5-p11"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl842", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008035809"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2004.02051.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008954850"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0304-3940(02)01423-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009175625"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0304-3940(02)01423-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009175625"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.95.4.1460", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009187647"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1143609", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010955799"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1746-4811-3-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013018295", 
          "https://doi.org/10.1186/1746-4811-3-7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gnh127", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014175856"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg033", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019342651"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1128691", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022607900"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm965", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023626877"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl976", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026152022"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.106.078626", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029269800"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl785", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029852377"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/43025", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030025869", 
          "https://doi.org/10.1038/43025"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/43025", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030025869", 
          "https://doi.org/10.1038/43025"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gng154", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034241213"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl767", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034528048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-8-369", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035728897", 
          "https://doi.org/10.1186/1471-2105-8-369"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-8-369", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035728897", 
          "https://doi.org/10.1186/1471-2105-8-369"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06148", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040664071", 
          "https://doi.org/10.1038/nature06148"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-179", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042074302", 
          "https://doi.org/10.1186/1471-2105-7-179"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10142-002-0065-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042777972", 
          "https://doi.org/10.1007/s10142-002-0065-3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-9-140", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045476497", 
          "https://doi.org/10.1186/1471-2164-9-140"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt0993-1026", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045863719", 
          "https://doi.org/10.1038/nbt0993-1026"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/25.17.3389", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047265454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkj155", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048447543"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-9-253", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049665949", 
          "https://doi.org/10.1186/1471-2105-9-253"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg094", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053722790"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1150646", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062457147"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074544770", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1083096756", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-12", 
    "datePublishedReg": "2008-12-01", 
    "description": "BACKGROUND: Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays.\nRESULTS: Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%.\nCONCLUSION: QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2105-9-465", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023786", 
        "issn": [
          "1471-2105"
        ], 
        "name": "BMC Bioinformatics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "QuantPrime \u2013 a flexible tool for reliable high-throughput primer design for quantitative PCR", 
    "pagination": "465", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "747c71df40fdc5f07f2fbbc8e18d92798591c1d73cc3d82017ea9127cc1de981"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18976492"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965194"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-9-465"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1024450931"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-9-465", 
      "https://app.dimensions.ai/details/publication/pub.1024450931"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T01:58", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8700_00000505.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2105-9-465"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-465'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-465'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-465'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-465'


 

This table displays all metadata directly associated to this object as RDF triples.

246 TRIPLES      21 PREDICATES      73 URIs      32 LITERALS      20 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-9-465 schema:about N03a62d1a6aad4e6ca0a580eeda87291e
2 N05177861677e46f2a7f56ec2fc906424
3 N05598ae3a1d8425cbf9ed2ebfe0c8e0d
4 N0d275260a45849629731c7bfabc6ad5c
5 N6852527ce52e40c58bddbb6988073b2b
6 N77d610306ac04662a2a2cf19ae5d34a1
7 N988e67dd903b4afbb19e2acfdf488e70
8 N9b5b6ae1bef0422e964fd79a60355d51
9 Na480b87bcf0f45ffa0b4e44eab567ee6
10 Nbb16830908244947ab06e5f17eb9ed88
11 Nc564a4c5fef4479ca31a79fe8e6b7224
12 anzsrc-for:06
13 anzsrc-for:0604
14 schema:author Nced5b21ec8444c8fa6cced51eb8fe87d
15 schema:citation sg:pub.10.1007/s10142-002-0065-3
16 sg:pub.10.1038/43025
17 sg:pub.10.1038/nature06148
18 sg:pub.10.1038/nbt0993-1026
19 sg:pub.10.1186/1471-2105-7-179
20 sg:pub.10.1186/1471-2105-8-369
21 sg:pub.10.1186/1471-2105-9-253
22 sg:pub.10.1186/1471-2164-9-140
23 sg:pub.10.1186/1746-4811-3-7
24 sg:pub.10.1186/gb-2004-5-5-p11
25 https://app.dimensions.ai/details/publication/pub.1074544770
26 https://app.dimensions.ai/details/publication/pub.1083096756
27 https://doi.org/10.1016/s0304-3940(02)01423-4
28 https://doi.org/10.1073/pnas.95.4.1460
29 https://doi.org/10.1093/nar/25.17.3389
30 https://doi.org/10.1093/nar/gkg033
31 https://doi.org/10.1093/nar/gkg094
32 https://doi.org/10.1093/nar/gkj155
33 https://doi.org/10.1093/nar/gkl767
34 https://doi.org/10.1093/nar/gkl785
35 https://doi.org/10.1093/nar/gkl842
36 https://doi.org/10.1093/nar/gkl976
37 https://doi.org/10.1093/nar/gkm306
38 https://doi.org/10.1093/nar/gkm965
39 https://doi.org/10.1093/nar/gkm999
40 https://doi.org/10.1093/nar/gng154
41 https://doi.org/10.1093/nar/gnh127
42 https://doi.org/10.1104/pp.106.078626
43 https://doi.org/10.1111/j.1365-313x.2004.02051.x
44 https://doi.org/10.1126/science.1128691
45 https://doi.org/10.1126/science.1143609
46 https://doi.org/10.1126/science.1150646
47 https://doi.org/10.1534/genetics.108.088336
48 schema:datePublished 2008-12
49 schema:datePublishedReg 2008-12-01
50 schema:description BACKGROUND: Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. RESULTS: Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%. CONCLUSION: QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.
51 schema:genre research_article
52 schema:inLanguage en
53 schema:isAccessibleForFree true
54 schema:isPartOf N519667acd2e14046b4ed3ccfe2a1734c
55 Nb49a3650f78b4596b2c35f645634344f
56 sg:journal.1023786
57 schema:name QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR
58 schema:pagination 465
59 schema:productId N1aad15ede4ce4e8a8661098c73dc931e
60 N4115b9555af048ae99234f43c50cd73c
61 N5d0ca940582c4cf9b458d8266bae3d80
62 N85e3ec75de67400f919421ee9ed5f63e
63 Ncfc571067c194428a1e5f6c0857204e7
64 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024450931
65 https://doi.org/10.1186/1471-2105-9-465
66 schema:sdDatePublished 2019-04-11T01:58
67 schema:sdLicense https://scigraph.springernature.com/explorer/license/
68 schema:sdPublisher N7f1886ef49934c1eba0b6ee42e65d771
69 schema:url http://link.springer.com/10.1186%2F1471-2105-9-465
70 sgo:license sg:explorer/license/
71 sgo:sdDataset articles
72 rdf:type schema:ScholarlyArticle
73 N03a62d1a6aad4e6ca0a580eeda87291e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name Sensitivity and Specificity
75 rdf:type schema:DefinedTerm
76 N05177861677e46f2a7f56ec2fc906424 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
77 schema:name Software
78 rdf:type schema:DefinedTerm
79 N05598ae3a1d8425cbf9ed2ebfe0c8e0d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
80 schema:name Base Sequence
81 rdf:type schema:DefinedTerm
82 N0d275260a45849629731c7bfabc6ad5c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
83 schema:name Molecular Sequence Data
84 rdf:type schema:DefinedTerm
85 N1aad15ede4ce4e8a8661098c73dc931e schema:name doi
86 schema:value 10.1186/1471-2105-9-465
87 rdf:type schema:PropertyValue
88 N4115b9555af048ae99234f43c50cd73c schema:name dimensions_id
89 schema:value pub.1024450931
90 rdf:type schema:PropertyValue
91 N47aa199efdd14de9a3f69b4bfb8a83ce rdf:first sg:person.01355415616.67
92 rdf:rest rdf:nil
93 N519667acd2e14046b4ed3ccfe2a1734c schema:volumeNumber 9
94 rdf:type schema:PublicationVolume
95 N5d0ca940582c4cf9b458d8266bae3d80 schema:name pubmed_id
96 schema:value 18976492
97 rdf:type schema:PropertyValue
98 N6852527ce52e40c58bddbb6988073b2b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Internet
100 rdf:type schema:DefinedTerm
101 N690b8c65a3754610985ff0c8e69d5715 rdf:first sg:person.01307302416.10
102 rdf:rest N47aa199efdd14de9a3f69b4bfb8a83ce
103 N77d610306ac04662a2a2cf19ae5d34a1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Nucleic Acid Probes
105 rdf:type schema:DefinedTerm
106 N7f1886ef49934c1eba0b6ee42e65d771 schema:name Springer Nature - SN SciGraph project
107 rdf:type schema:Organization
108 N85e3ec75de67400f919421ee9ed5f63e schema:name nlm_unique_id
109 schema:value 100965194
110 rdf:type schema:PropertyValue
111 N988e67dd903b4afbb19e2acfdf488e70 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name Sequence Analysis, DNA
113 rdf:type schema:DefinedTerm
114 N9b5b6ae1bef0422e964fd79a60355d51 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Databases, Genetic
116 rdf:type schema:DefinedTerm
117 Na480b87bcf0f45ffa0b4e44eab567ee6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
118 schema:name User-Computer Interface
119 rdf:type schema:DefinedTerm
120 Nb49a3650f78b4596b2c35f645634344f schema:issueNumber 1
121 rdf:type schema:PublicationIssue
122 Nbb16830908244947ab06e5f17eb9ed88 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name DNA Primers
124 rdf:type schema:DefinedTerm
125 Nc0321bab7b3c4a31ac30bd5ade29f994 rdf:first sg:person.01073755136.20
126 rdf:rest N690b8c65a3754610985ff0c8e69d5715
127 Nc564a4c5fef4479ca31a79fe8e6b7224 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name Polymerase Chain Reaction
129 rdf:type schema:DefinedTerm
130 Nced5b21ec8444c8fa6cced51eb8fe87d rdf:first sg:person.0764644363.16
131 rdf:rest Nc0321bab7b3c4a31ac30bd5ade29f994
132 Ncfc571067c194428a1e5f6c0857204e7 schema:name readcube_id
133 schema:value 747c71df40fdc5f07f2fbbc8e18d92798591c1d73cc3d82017ea9127cc1de981
134 rdf:type schema:PropertyValue
135 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
136 schema:name Biological Sciences
137 rdf:type schema:DefinedTerm
138 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
139 schema:name Genetics
140 rdf:type schema:DefinedTerm
141 sg:journal.1023786 schema:issn 1471-2105
142 schema:name BMC Bioinformatics
143 rdf:type schema:Periodical
144 sg:person.01073755136.20 schema:affiliation https://www.grid.ac/institutes/grid.11866.38
145 schema:familyName Kwasniewski
146 schema:givenName Miroslaw
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073755136.20
148 rdf:type schema:Person
149 sg:person.01307302416.10 schema:affiliation https://www.grid.ac/institutes/grid.11348.3f
150 schema:familyName Riaño-Pachón
151 schema:givenName Diego Mauricio
152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01307302416.10
153 rdf:type schema:Person
154 sg:person.01355415616.67 schema:affiliation https://www.grid.ac/institutes/grid.11348.3f
155 schema:familyName Mueller-Roeber
156 schema:givenName Bernd
157 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355415616.67
158 rdf:type schema:Person
159 sg:person.0764644363.16 schema:affiliation https://www.grid.ac/institutes/grid.11348.3f
160 schema:familyName Arvidsson
161 schema:givenName Samuel
162 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764644363.16
163 rdf:type schema:Person
164 sg:pub.10.1007/s10142-002-0065-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042777972
165 https://doi.org/10.1007/s10142-002-0065-3
166 rdf:type schema:CreativeWork
167 sg:pub.10.1038/43025 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030025869
168 https://doi.org/10.1038/43025
169 rdf:type schema:CreativeWork
170 sg:pub.10.1038/nature06148 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040664071
171 https://doi.org/10.1038/nature06148
172 rdf:type schema:CreativeWork
173 sg:pub.10.1038/nbt0993-1026 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045863719
174 https://doi.org/10.1038/nbt0993-1026
175 rdf:type schema:CreativeWork
176 sg:pub.10.1186/1471-2105-7-179 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042074302
177 https://doi.org/10.1186/1471-2105-7-179
178 rdf:type schema:CreativeWork
179 sg:pub.10.1186/1471-2105-8-369 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035728897
180 https://doi.org/10.1186/1471-2105-8-369
181 rdf:type schema:CreativeWork
182 sg:pub.10.1186/1471-2105-9-253 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049665949
183 https://doi.org/10.1186/1471-2105-9-253
184 rdf:type schema:CreativeWork
185 sg:pub.10.1186/1471-2164-9-140 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045476497
186 https://doi.org/10.1186/1471-2164-9-140
187 rdf:type schema:CreativeWork
188 sg:pub.10.1186/1746-4811-3-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013018295
189 https://doi.org/10.1186/1746-4811-3-7
190 rdf:type schema:CreativeWork
191 sg:pub.10.1186/gb-2004-5-5-p11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004632209
192 https://doi.org/10.1186/gb-2004-5-5-p11
193 rdf:type schema:CreativeWork
194 https://app.dimensions.ai/details/publication/pub.1074544770 schema:CreativeWork
195 https://app.dimensions.ai/details/publication/pub.1083096756 schema:CreativeWork
196 https://doi.org/10.1016/s0304-3940(02)01423-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009175625
197 rdf:type schema:CreativeWork
198 https://doi.org/10.1073/pnas.95.4.1460 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009187647
199 rdf:type schema:CreativeWork
200 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
201 rdf:type schema:CreativeWork
202 https://doi.org/10.1093/nar/gkg033 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019342651
203 rdf:type schema:CreativeWork
204 https://doi.org/10.1093/nar/gkg094 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053722790
205 rdf:type schema:CreativeWork
206 https://doi.org/10.1093/nar/gkj155 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048447543
207 rdf:type schema:CreativeWork
208 https://doi.org/10.1093/nar/gkl767 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034528048
209 rdf:type schema:CreativeWork
210 https://doi.org/10.1093/nar/gkl785 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029852377
211 rdf:type schema:CreativeWork
212 https://doi.org/10.1093/nar/gkl842 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008035809
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1093/nar/gkl976 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026152022
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1093/nar/gkm306 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003651676
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1093/nar/gkm965 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023626877
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1093/nar/gkm999 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004115570
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1093/nar/gng154 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034241213
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1093/nar/gnh127 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014175856
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1104/pp.106.078626 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029269800
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1111/j.1365-313x.2004.02051.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1008954850
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1126/science.1128691 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022607900
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1126/science.1143609 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010955799
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1126/science.1150646 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062457147
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1534/genetics.108.088336 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003655378
237 rdf:type schema:CreativeWork
238 https://www.grid.ac/institutes/grid.11348.3f schema:alternateName University of Potsdam
239 schema:name Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam-Golm, Germany
240 Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
241 rdf:type schema:Organization
242 https://www.grid.ac/institutes/grid.11866.38 schema:alternateName University of Silesia
243 schema:name Department of Genetics, University of Silesia, Jagiellonska 28, 40032, Katowice, Poland
244 Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam-Golm, Germany
245 Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
246 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...