Whole-genome sequencing and variant discovery in C. elegans View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2008-02

AUTHORS

LaDeana W Hillier, Gabor T Marth, Aaron R Quinlan, David Dooling, Ginger Fewell, Derek Barnett, Paul Fox, Jarret I Glasscock, Matthew Hickenbotham, Weichun Huang, Vincent J Magrini, Ryan J Richt, Sacha N Sander, Donald A Stewart, Michael Stromberg, Eric F Tsung, Todd Wylie, Tim Schedl, Richard K Wilson, Elaine R Mardis

ABSTRACT

Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms. More... »

PAGES

183-188

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth.1179

DOI

http://dx.doi.org/10.1038/nmeth.1179

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1001773338

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18204455


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": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Caenorhabditis elegans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosome Mapping", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Mutational Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genetic Variation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymorphism, Single Nucleotide", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hillier", 
        "givenName": "LaDeana W", 
        "id": "sg:person.01014313442.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01014313442.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Boston College", 
          "id": "https://www.grid.ac/institutes/grid.208226.c", 
          "name": [
            "Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Marth", 
        "givenName": "Gabor T", 
        "id": "sg:person.0617524562.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0617524562.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Boston College", 
          "id": "https://www.grid.ac/institutes/grid.208226.c", 
          "name": [
            "Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Quinlan", 
        "givenName": "Aaron R", 
        "id": "sg:person.0612231705.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0612231705.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dooling", 
        "givenName": "David", 
        "id": "sg:person.01327105734.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01327105734.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fewell", 
        "givenName": "Ginger", 
        "id": "sg:person.0603501634.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0603501634.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Boston College", 
          "id": "https://www.grid.ac/institutes/grid.208226.c", 
          "name": [
            "Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Barnett", 
        "givenName": "Derek", 
        "id": "sg:person.0651615034.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0651615034.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fox", 
        "givenName": "Paul", 
        "id": "sg:person.01022220712.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022220712.89"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Glasscock", 
        "givenName": "Jarret I", 
        "id": "sg:person.01325554650.54", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01325554650.54"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hickenbotham", 
        "givenName": "Matthew", 
        "id": "sg:person.01257441450.64", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01257441450.64"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Boston College", 
          "id": "https://www.grid.ac/institutes/grid.208226.c", 
          "name": [
            "Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Huang", 
        "givenName": "Weichun", 
        "id": "sg:person.01072661551.21", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01072661551.21"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Magrini", 
        "givenName": "Vincent J", 
        "id": "sg:person.01030001224.78", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030001224.78"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Richt", 
        "givenName": "Ryan J", 
        "id": "sg:person.01216520434.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01216520434.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sander", 
        "givenName": "Sacha N", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Boston College", 
          "id": "https://www.grid.ac/institutes/grid.208226.c", 
          "name": [
            "Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stewart", 
        "givenName": "Donald A", 
        "id": "sg:person.01205075574.75", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01205075574.75"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Boston College", 
          "id": "https://www.grid.ac/institutes/grid.208226.c", 
          "name": [
            "Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stromberg", 
        "givenName": "Michael", 
        "id": "sg:person.01343130662.03", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01343130662.03"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Boston College", 
          "id": "https://www.grid.ac/institutes/grid.208226.c", 
          "name": [
            "Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tsung", 
        "givenName": "Eric F", 
        "id": "sg:person.0777523030.35", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777523030.35"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wylie", 
        "givenName": "Todd", 
        "id": "sg:person.0626250070.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0626250070.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schedl", 
        "givenName": "Tim", 
        "id": "sg:person.0600467126.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0600467126.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wilson", 
        "givenName": "Richard K", 
        "id": "sg:person.013076541047.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013076541047.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mardis", 
        "givenName": "Elaine R", 
        "id": "sg:person.01023627236.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023627236.33"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/70570", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011138564", 
          "https://doi.org/10.1038/70570"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/70570", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011138564", 
          "https://doi.org/10.1038/70570"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013534924", 
          "https://doi.org/10.1038/nature03001"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013534924", 
          "https://doi.org/10.1038/nature03001"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1562", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014017119", 
          "https://doi.org/10.1038/ng1562"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1562", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014017119", 
          "https://doi.org/10.1038/ng1562"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1562", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014017119", 
          "https://doi.org/10.1038/ng1562"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pbio.0000045", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014837158"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.8.3.195", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018564763"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1385/1-59259-235-x:029", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019677666", 
          "https://doi.org/10.1385/1-59259-235-x:029"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.gr-1471r", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022802855"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1925", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023481670", 
          "https://doi.org/10.1038/ng1925"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1925", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023481670", 
          "https://doi.org/10.1038/ng1925"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1746", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026251895", 
          "https://doi.org/10.1038/ng1746"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1746", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026251895", 
          "https://doi.org/10.1038/ng1746"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0959-437x(96)80030-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032901070"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msg044", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034268093"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh066", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035810379"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl818", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042758114"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057062", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042854081", 
          "https://doi.org/10.1038/35057062"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057062", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042854081", 
          "https://doi.org/10.1038/35057062"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/sqb.1993.058.01.043", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060406505"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.282.5396.2012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062563514"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1083083595", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-02", 
    "datePublishedReg": "2008-02-01", 
    "description": "Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nmeth.1179", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2529243", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2699329", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2517087", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1033763", 
        "issn": [
          "1548-7091", 
          "1548-7105"
        ], 
        "name": "Nature Methods", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "2", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "5"
      }
    ], 
    "name": "Whole-genome sequencing and variant discovery in C. elegans", 
    "pagination": "183-188", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "087212643fdec93b3964eef1a49e4bab8cb2efe23b56380a7702ea12bd774d98"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18204455"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101215604"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nmeth.1179"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1001773338"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nmeth.1179", 
      "https://app.dimensions.ai/details/publication/pub.1001773338"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T00:54", 
    "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_8697_00000421.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/articles/nmeth.1179"
  }
]
 

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.10.1038/nmeth.1179'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nmeth.1179'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nmeth.1179'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nmeth.1179'


 

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

303 TRIPLES      21 PREDICATES      55 URIs      30 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nmeth.1179 schema:about N1e37243b40e14b5d803fe3aa830505c5
2 N21d38d869d7a4f239d32d2b360921da6
3 N306f6e9c87a240979f10cb0748e0de06
4 N7f7456a39bbe4865a6040f2dcf08d06f
5 N84de36fdeb02499ea6240b26aca6e9d4
6 N961c5ee9fd9e4b6a83acde20ebb4e6bd
7 N99a47f7d5f644a7790ed58548ba65abd
8 Ncd4bd29c861c4af8a3cc07f352151276
9 Nf63cd9165e67429b9c18f6f4149002f9
10 anzsrc-for:06
11 anzsrc-for:0604
12 schema:author Nfbb1fe9c270f40d1b331d10083070cad
13 schema:citation sg:pub.10.1038/35057062
14 sg:pub.10.1038/70570
15 sg:pub.10.1038/nature03001
16 sg:pub.10.1038/ng1562
17 sg:pub.10.1038/ng1746
18 sg:pub.10.1038/ng1925
19 sg:pub.10.1385/1-59259-235-x:029
20 https://app.dimensions.ai/details/publication/pub.1083083595
21 https://doi.org/10.1016/s0959-437x(96)80030-x
22 https://doi.org/10.1093/molbev/msg044
23 https://doi.org/10.1093/nar/gkh066
24 https://doi.org/10.1093/nar/gkl818
25 https://doi.org/10.1101/gr.8.3.195
26 https://doi.org/10.1101/gr.gr-1471r
27 https://doi.org/10.1101/sqb.1993.058.01.043
28 https://doi.org/10.1126/science.282.5396.2012
29 https://doi.org/10.1371/journal.pbio.0000045
30 schema:datePublished 2008-02
31 schema:datePublishedReg 2008-02-01
32 schema:description Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms.
33 schema:genre research_article
34 schema:inLanguage en
35 schema:isAccessibleForFree false
36 schema:isPartOf N13249ab0b01a4bbdb7fe0d2d560414ac
37 N134fc8704a4d4d38b3a7d3cc92fdfc38
38 sg:journal.1033763
39 schema:name Whole-genome sequencing and variant discovery in C. elegans
40 schema:pagination 183-188
41 schema:productId N17b5948e9bf8419daeb4def51582f65a
42 N558bc4ac8a38455183e9bae0850d2617
43 N69bffef854964fb0ba44e68897901590
44 N8f558a05426d4da086b21180b64dbb0c
45 Nf5380bc2faed4d37bc9bb68e36e8a338
46 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001773338
47 https://doi.org/10.1038/nmeth.1179
48 schema:sdDatePublished 2019-04-11T00:54
49 schema:sdLicense https://scigraph.springernature.com/explorer/license/
50 schema:sdPublisher N436aaae2fad345a287e7e66a6d3956bc
51 schema:url http://www.nature.com/articles/nmeth.1179
52 sgo:license sg:explorer/license/
53 sgo:sdDataset articles
54 rdf:type schema:ScholarlyArticle
55 N08d3173bd4b5463c8295ae1fe9f3c672 rdf:first sg:person.01022220712.89
56 rdf:rest Nead0f11526ab41b0a9476b49a60c9b23
57 N0ab6049d9d414866bbd7388316ac60f0 rdf:first sg:person.0600467126.05
58 rdf:rest Ndf5544820f7948f9a8f7deeb4e9be138
59 N0b0c512bb3df4041846442ab631a17c8 rdf:first sg:person.0603501634.38
60 rdf:rest N36f32fdf05504aee99f7389637c56b8a
61 N0bc2e6791a714ebaaf6f96ea988b7a21 rdf:first sg:person.01327105734.20
62 rdf:rest N0b0c512bb3df4041846442ab631a17c8
63 N13249ab0b01a4bbdb7fe0d2d560414ac schema:issueNumber 2
64 rdf:type schema:PublicationIssue
65 N134fc8704a4d4d38b3a7d3cc92fdfc38 schema:volumeNumber 5
66 rdf:type schema:PublicationVolume
67 N17b5948e9bf8419daeb4def51582f65a schema:name pubmed_id
68 schema:value 18204455
69 rdf:type schema:PropertyValue
70 N196239ef6819437aaa84d2208b2bce92 rdf:first sg:person.01257441450.64
71 rdf:rest Nb0e22c9dc45b45208ee46690b242426f
72 N1cca8caacf044fadbe6cc93d7dcfa707 rdf:first sg:person.01205075574.75
73 rdf:rest N34f7c972ab3848c7aa552e60a44cfc07
74 N1cd165ba575446d8b79d651e86b9aa26 rdf:first sg:person.0612231705.45
75 rdf:rest N0bc2e6791a714ebaaf6f96ea988b7a21
76 N1e37243b40e14b5d803fe3aa830505c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
77 schema:name DNA Mutational Analysis
78 rdf:type schema:DefinedTerm
79 N2017eef6fbd14cd18bb2ca36b4fee4ab rdf:first sg:person.0617524562.14
80 rdf:rest N1cd165ba575446d8b79d651e86b9aa26
81 N21d38d869d7a4f239d32d2b360921da6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
82 schema:name Caenorhabditis elegans
83 rdf:type schema:DefinedTerm
84 N220f15aa1aa845e298b75dcbfe958589 rdf:first sg:person.01216520434.20
85 rdf:rest Nf30b39f5ed86464fb6962aef775a3df3
86 N306f6e9c87a240979f10cb0748e0de06 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
87 schema:name Sequence Analysis, DNA
88 rdf:type schema:DefinedTerm
89 N34f7c972ab3848c7aa552e60a44cfc07 rdf:first sg:person.01343130662.03
90 rdf:rest N596359c1c11e4370a630459f773be52f
91 N36f32fdf05504aee99f7389637c56b8a rdf:first sg:person.0651615034.20
92 rdf:rest N08d3173bd4b5463c8295ae1fe9f3c672
93 N436aaae2fad345a287e7e66a6d3956bc schema:name Springer Nature - SN SciGraph project
94 rdf:type schema:Organization
95 N43ad868f18354f66aff2e6ee510601f9 rdf:first sg:person.01023627236.33
96 rdf:rest rdf:nil
97 N558bc4ac8a38455183e9bae0850d2617 schema:name readcube_id
98 schema:value 087212643fdec93b3964eef1a49e4bab8cb2efe23b56380a7702ea12bd774d98
99 rdf:type schema:PropertyValue
100 N596359c1c11e4370a630459f773be52f rdf:first sg:person.0777523030.35
101 rdf:rest Ncb08ce65234f4ead9b4ac21223d58590
102 N69bffef854964fb0ba44e68897901590 schema:name nlm_unique_id
103 schema:value 101215604
104 rdf:type schema:PropertyValue
105 N7f7456a39bbe4865a6040f2dcf08d06f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name Genetic Variation
107 rdf:type schema:DefinedTerm
108 N84de36fdeb02499ea6240b26aca6e9d4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
109 schema:name Base Sequence
110 rdf:type schema:DefinedTerm
111 N8f558a05426d4da086b21180b64dbb0c schema:name dimensions_id
112 schema:value pub.1001773338
113 rdf:type schema:PropertyValue
114 N961c5ee9fd9e4b6a83acde20ebb4e6bd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Molecular Sequence Data
116 rdf:type schema:DefinedTerm
117 N99a47f7d5f644a7790ed58548ba65abd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
118 schema:name Chromosome Mapping
119 rdf:type schema:DefinedTerm
120 Nb0e22c9dc45b45208ee46690b242426f rdf:first sg:person.01072661551.21
121 rdf:rest Nec83256d5cd3445f829d39acf1ca3e86
122 Nc27daf8f235c480bb700e790fe6bbb08 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
123 schema:familyName Sander
124 schema:givenName Sacha N
125 rdf:type schema:Person
126 Ncb08ce65234f4ead9b4ac21223d58590 rdf:first sg:person.0626250070.02
127 rdf:rest N0ab6049d9d414866bbd7388316ac60f0
128 Ncd4bd29c861c4af8a3cc07f352151276 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Polymorphism, Single Nucleotide
130 rdf:type schema:DefinedTerm
131 Ndf5544820f7948f9a8f7deeb4e9be138 rdf:first sg:person.013076541047.38
132 rdf:rest N43ad868f18354f66aff2e6ee510601f9
133 Nead0f11526ab41b0a9476b49a60c9b23 rdf:first sg:person.01325554650.54
134 rdf:rest N196239ef6819437aaa84d2208b2bce92
135 Nec83256d5cd3445f829d39acf1ca3e86 rdf:first sg:person.01030001224.78
136 rdf:rest N220f15aa1aa845e298b75dcbfe958589
137 Nf30b39f5ed86464fb6962aef775a3df3 rdf:first Nc27daf8f235c480bb700e790fe6bbb08
138 rdf:rest N1cca8caacf044fadbe6cc93d7dcfa707
139 Nf5380bc2faed4d37bc9bb68e36e8a338 schema:name doi
140 schema:value 10.1038/nmeth.1179
141 rdf:type schema:PropertyValue
142 Nf63cd9165e67429b9c18f6f4149002f9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
143 schema:name Animals
144 rdf:type schema:DefinedTerm
145 Nfbb1fe9c270f40d1b331d10083070cad rdf:first sg:person.01014313442.46
146 rdf:rest N2017eef6fbd14cd18bb2ca36b4fee4ab
147 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
148 schema:name Biological Sciences
149 rdf:type schema:DefinedTerm
150 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
151 schema:name Genetics
152 rdf:type schema:DefinedTerm
153 sg:grant.2517087 http://pending.schema.org/fundedItem sg:pub.10.1038/nmeth.1179
154 rdf:type schema:MonetaryGrant
155 sg:grant.2529243 http://pending.schema.org/fundedItem sg:pub.10.1038/nmeth.1179
156 rdf:type schema:MonetaryGrant
157 sg:grant.2699329 http://pending.schema.org/fundedItem sg:pub.10.1038/nmeth.1179
158 rdf:type schema:MonetaryGrant
159 sg:journal.1033763 schema:issn 1548-7091
160 1548-7105
161 schema:name Nature Methods
162 rdf:type schema:Periodical
163 sg:person.01014313442.46 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
164 schema:familyName Hillier
165 schema:givenName LaDeana W
166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01014313442.46
167 rdf:type schema:Person
168 sg:person.01022220712.89 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
169 schema:familyName Fox
170 schema:givenName Paul
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022220712.89
172 rdf:type schema:Person
173 sg:person.01023627236.33 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
174 schema:familyName Mardis
175 schema:givenName Elaine R
176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023627236.33
177 rdf:type schema:Person
178 sg:person.01030001224.78 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
179 schema:familyName Magrini
180 schema:givenName Vincent J
181 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030001224.78
182 rdf:type schema:Person
183 sg:person.01072661551.21 schema:affiliation https://www.grid.ac/institutes/grid.208226.c
184 schema:familyName Huang
185 schema:givenName Weichun
186 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01072661551.21
187 rdf:type schema:Person
188 sg:person.01205075574.75 schema:affiliation https://www.grid.ac/institutes/grid.208226.c
189 schema:familyName Stewart
190 schema:givenName Donald A
191 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01205075574.75
192 rdf:type schema:Person
193 sg:person.01216520434.20 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
194 schema:familyName Richt
195 schema:givenName Ryan J
196 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01216520434.20
197 rdf:type schema:Person
198 sg:person.01257441450.64 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
199 schema:familyName Hickenbotham
200 schema:givenName Matthew
201 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01257441450.64
202 rdf:type schema:Person
203 sg:person.013076541047.38 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
204 schema:familyName Wilson
205 schema:givenName Richard K
206 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013076541047.38
207 rdf:type schema:Person
208 sg:person.01325554650.54 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
209 schema:familyName Glasscock
210 schema:givenName Jarret I
211 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01325554650.54
212 rdf:type schema:Person
213 sg:person.01327105734.20 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
214 schema:familyName Dooling
215 schema:givenName David
216 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01327105734.20
217 rdf:type schema:Person
218 sg:person.01343130662.03 schema:affiliation https://www.grid.ac/institutes/grid.208226.c
219 schema:familyName Stromberg
220 schema:givenName Michael
221 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01343130662.03
222 rdf:type schema:Person
223 sg:person.0600467126.05 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
224 schema:familyName Schedl
225 schema:givenName Tim
226 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0600467126.05
227 rdf:type schema:Person
228 sg:person.0603501634.38 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
229 schema:familyName Fewell
230 schema:givenName Ginger
231 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0603501634.38
232 rdf:type schema:Person
233 sg:person.0612231705.45 schema:affiliation https://www.grid.ac/institutes/grid.208226.c
234 schema:familyName Quinlan
235 schema:givenName Aaron R
236 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0612231705.45
237 rdf:type schema:Person
238 sg:person.0617524562.14 schema:affiliation https://www.grid.ac/institutes/grid.208226.c
239 schema:familyName Marth
240 schema:givenName Gabor T
241 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0617524562.14
242 rdf:type schema:Person
243 sg:person.0626250070.02 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
244 schema:familyName Wylie
245 schema:givenName Todd
246 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0626250070.02
247 rdf:type schema:Person
248 sg:person.0651615034.20 schema:affiliation https://www.grid.ac/institutes/grid.208226.c
249 schema:familyName Barnett
250 schema:givenName Derek
251 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0651615034.20
252 rdf:type schema:Person
253 sg:person.0777523030.35 schema:affiliation https://www.grid.ac/institutes/grid.208226.c
254 schema:familyName Tsung
255 schema:givenName Eric F
256 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777523030.35
257 rdf:type schema:Person
258 sg:pub.10.1038/35057062 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042854081
259 https://doi.org/10.1038/35057062
260 rdf:type schema:CreativeWork
261 sg:pub.10.1038/70570 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011138564
262 https://doi.org/10.1038/70570
263 rdf:type schema:CreativeWork
264 sg:pub.10.1038/nature03001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013534924
265 https://doi.org/10.1038/nature03001
266 rdf:type schema:CreativeWork
267 sg:pub.10.1038/ng1562 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014017119
268 https://doi.org/10.1038/ng1562
269 rdf:type schema:CreativeWork
270 sg:pub.10.1038/ng1746 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026251895
271 https://doi.org/10.1038/ng1746
272 rdf:type schema:CreativeWork
273 sg:pub.10.1038/ng1925 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023481670
274 https://doi.org/10.1038/ng1925
275 rdf:type schema:CreativeWork
276 sg:pub.10.1385/1-59259-235-x:029 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019677666
277 https://doi.org/10.1385/1-59259-235-x:029
278 rdf:type schema:CreativeWork
279 https://app.dimensions.ai/details/publication/pub.1083083595 schema:CreativeWork
280 https://doi.org/10.1016/s0959-437x(96)80030-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1032901070
281 rdf:type schema:CreativeWork
282 https://doi.org/10.1093/molbev/msg044 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034268093
283 rdf:type schema:CreativeWork
284 https://doi.org/10.1093/nar/gkh066 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035810379
285 rdf:type schema:CreativeWork
286 https://doi.org/10.1093/nar/gkl818 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042758114
287 rdf:type schema:CreativeWork
288 https://doi.org/10.1101/gr.8.3.195 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018564763
289 rdf:type schema:CreativeWork
290 https://doi.org/10.1101/gr.gr-1471r schema:sameAs https://app.dimensions.ai/details/publication/pub.1022802855
291 rdf:type schema:CreativeWork
292 https://doi.org/10.1101/sqb.1993.058.01.043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060406505
293 rdf:type schema:CreativeWork
294 https://doi.org/10.1126/science.282.5396.2012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062563514
295 rdf:type schema:CreativeWork
296 https://doi.org/10.1371/journal.pbio.0000045 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014837158
297 rdf:type schema:CreativeWork
298 https://www.grid.ac/institutes/grid.208226.c schema:alternateName Boston College
299 schema:name Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA.
300 rdf:type schema:Organization
301 https://www.grid.ac/institutes/grid.4367.6 schema:alternateName Washington University in St. Louis
302 schema:name Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA.
303 rdf:type schema:Organization
 




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


...