Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-12

AUTHORS

Heesun Shin, Martin Hirst, Matthew N Bainbridge, Vincent Magrini, Elaine Mardis, Donald G Moerman, Marco A Marra, David L Baillie, Steven JM Jones

ABSTRACT

BACKGROUND: We have applied a high-throughput pyrosequencing technology for transcriptome profiling of Caenorhabditis elegans in its first larval stage. Using this approach, we have generated a large amount of data for expressed sequence tags, which provides an opportunity for the discovery of putative novel transcripts and alternative splice variants that could be developmentally specific to the first larval stage. This work also demonstrates the successful and efficient application of a next generation sequencing methodology. RESULTS: We have generated over 30 million bases of novel expressed sequence tags from first larval stage worms utilizing high-throughput sequencing technology. We have shown that approximately 14% of the newly sequenced expressed sequence tags map completely or partially to genomic regions where there are no annotated genes or splice variants and therefore, imply that these are novel genetic structures. Expressed sequence tags, which map to intergenic (around 1000) and intronic regions (around 580), may represent novel transcribed regions, such as unannotated or unrecognized small protein-coding or non-protein-coding genes or splice variants. Expressed sequence tags, which map across intron-exon boundaries (around 300), indicate possible alternative splice sites, while expressed sequence tags, which map near the ends of known transcripts (around 600), suggest extension of the coding or untranslated regions. We have also discovered that intergenic and intronic expressed sequence tags, which are well conserved across different nematode species, are likely to represent non-coding RNAs. Lastly, we have incorporated available serial analysis of gene expression data generated from first larval stage worms, in order to predict novel transcripts that might be specifically or predominantly expressed in the first larval stage. CONCLUSION: We have demonstrated the use of a high-throughput sequencing methodology to efficiently produce a snap-shot of transcriptional activities occurring in the first larval stage of C. elegans development. Such application of this new sequencing technique allows for high-throughput, genome-wide experimental verification of known and novel transcripts. This study provides a more complete C. elegans transcriptome profile and, furthermore, gives insight into the evolutionary and biological complexity of this organism. More... »

PAGES

30

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1741-7007-6-30

DOI

http://dx.doi.org/10.1186/1741-7007-6-30

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1048431115

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18611272


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 Composition", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Caenorhabditis", 
        "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": "Conserved Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Exons", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Expressed Sequence Tags", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Profiling", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Helminth", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Introns", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Larva", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Isoforms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Species Specificity", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "BC Cancer Agency", 
          "id": "https://www.grid.ac/institutes/grid.248762.d", 
          "name": [
            "Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada", 
            "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shin", 
        "givenName": "Heesun", 
        "id": "sg:person.01034505366.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01034505366.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "BC Cancer Agency", 
          "id": "https://www.grid.ac/institutes/grid.248762.d", 
          "name": [
            "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hirst", 
        "givenName": "Martin", 
        "id": "sg:person.0601713543.66", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601713543.66"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "BC Cancer Agency", 
          "id": "https://www.grid.ac/institutes/grid.248762.d", 
          "name": [
            "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bainbridge", 
        "givenName": "Matthew N", 
        "id": "sg:person.01070416716.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070416716.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Washington University in St. Louis", 
          "id": "https://www.grid.ac/institutes/grid.4367.6", 
          "name": [
            "Genome Sequencing Center, Washington University School of Medicine, St Louis, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Magrini", 
        "givenName": "Vincent", 
        "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": [
            "Genome Sequencing Center, Washington University School of Medicine, St Louis, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mardis", 
        "givenName": "Elaine", 
        "id": "sg:person.01023627236.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023627236.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of British Columbia", 
          "id": "https://www.grid.ac/institutes/grid.17091.3e", 
          "name": [
            "Department of Zoology, University of British Columbia, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Moerman", 
        "givenName": "Donald G", 
        "id": "sg:person.01305401161.47", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305401161.47"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "BC Cancer Agency", 
          "id": "https://www.grid.ac/institutes/grid.248762.d", 
          "name": [
            "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Marra", 
        "givenName": "Marco A", 
        "id": "sg:person.01150455763.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01150455763.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Simon Fraser University", 
          "id": "https://www.grid.ac/institutes/grid.61971.38", 
          "name": [
            "Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Baillie", 
        "givenName": "David L", 
        "id": "sg:person.01315322630.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315322630.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "BC Cancer Agency", 
          "id": "https://www.grid.ac/institutes/grid.248762.d", 
          "name": [
            "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jones", 
        "givenName": "Steven JM", 
        "id": "sg:person.011076371162.80", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011076371162.80"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1101/gad.11.12.1493", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001434602"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.873003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002115475"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrm1648", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003259347", 
          "https://doi.org/10.1038/nrm1648"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrm1648", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003259347", 
          "https://doi.org/10.1038/nrm1648"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrm1648", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003259347", 
          "https://doi.org/10.1038/nrm1648"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.4139206", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004882909"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/emboj/18.19.5399", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005082025"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/jez.b.21086", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007388294"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/jez.b.21086", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007388294"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.6984908", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010761083"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1011982932645", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011731095", 
          "https://doi.org/10.1023/a:1011982932645"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/24.1.21", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013074371"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/sqb.2006.71.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013387185"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.1390403", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014635681"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0409169102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016701541"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03959", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021574562", 
          "https://doi.org/10.1038/nature03959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03959", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021574562", 
          "https://doi.org/10.1038/nature03959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bth088", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022171874"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1261/rna.7135204", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023833580"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.2722704", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024280946"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng0102-13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025102244", 
          "https://doi.org/10.1038/ng0102-13"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng0102-13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025102244", 
          "https://doi.org/10.1038/ng0102-13"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-7-246", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026547515", 
          "https://doi.org/10.1186/1471-2164-7-246"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2007.03244.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028076986"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.freeradbiomed.2006.08.024", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036491564"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.8.3.186", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038920266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-7-272", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040475066", 
          "https://doi.org/10.1186/1471-2164-7-272"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-2-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046362248", 
          "https://doi.org/10.1186/1471-2105-2-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046557993", 
          "https://doi.org/10.1038/nature01012"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046557993", 
          "https://doi.org/10.1038/nature01012"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.6611807", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047705066"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.5488207", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048766691"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/sqb.2003.68.159", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060415953"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1061603", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062445115"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1895/wormbook.1.1.1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1068724073"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/29.19.3928", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1074886589"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-12", 
    "datePublishedReg": "2008-12-01", 
    "description": "BACKGROUND: We have applied a high-throughput pyrosequencing technology for transcriptome profiling of Caenorhabditis elegans in its first larval stage. Using this approach, we have generated a large amount of data for expressed sequence tags, which provides an opportunity for the discovery of putative novel transcripts and alternative splice variants that could be developmentally specific to the first larval stage. This work also demonstrates the successful and efficient application of a next generation sequencing methodology.\nRESULTS: We have generated over 30 million bases of novel expressed sequence tags from first larval stage worms utilizing high-throughput sequencing technology. We have shown that approximately 14% of the newly sequenced expressed sequence tags map completely or partially to genomic regions where there are no annotated genes or splice variants and therefore, imply that these are novel genetic structures. Expressed sequence tags, which map to intergenic (around 1000) and intronic regions (around 580), may represent novel transcribed regions, such as unannotated or unrecognized small protein-coding or non-protein-coding genes or splice variants. Expressed sequence tags, which map across intron-exon boundaries (around 300), indicate possible alternative splice sites, while expressed sequence tags, which map near the ends of known transcripts (around 600), suggest extension of the coding or untranslated regions. We have also discovered that intergenic and intronic expressed sequence tags, which are well conserved across different nematode species, are likely to represent non-coding RNAs. Lastly, we have incorporated available serial analysis of gene expression data generated from first larval stage worms, in order to predict novel transcripts that might be specifically or predominantly expressed in the first larval stage.\nCONCLUSION: We have demonstrated the use of a high-throughput sequencing methodology to efficiently produce a snap-shot of transcriptional activities occurring in the first larval stage of C. elegans development. Such application of this new sequencing technique allows for high-throughput, genome-wide experimental verification of known and novel transcripts. This study provides a more complete C. elegans transcriptome profile and, furthermore, gives insight into the evolutionary and biological complexity of this organism.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1741-7007-6-30", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1032884", 
        "issn": [
          "1478-5854", 
          "1741-7007"
        ], 
        "name": "BMC Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "6"
      }
    ], 
    "name": "Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags", 
    "pagination": "30", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "e6b7a4b248d30551efa2b598547dd7a7b9a26e22099360ba47d507f55a85678b"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18611272"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101190720"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1741-7007-6-30"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1048431115"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1741-7007-6-30", 
      "https://app.dimensions.ai/details/publication/pub.1048431115"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T20:48", 
    "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_8684_00000516.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1741-7007-6-30"
  }
]
 

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.10.1186/1741-7007-6-30'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1741-7007-6-30'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1741-7007-6-30'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1741-7007-6-30'


 

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

293 TRIPLES      21 PREDICATES      74 URIs      36 LITERALS      24 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1741-7007-6-30 schema:about N615daf9b345d43499c283b1103672c0b
2 N6d6eeb525b1a4720a3f9111f592debcb
3 N8f3d494297b84d93bf920347547c1390
4 N926110dcb7cb44a3a960e5bea623c854
5 Nbf62a12794f242ddaeb734981a0f7d56
6 Nc1ad2a5752884947a21484ea191d3d17
7 Nc3f526986d5c4260a0aa5e5359329795
8 Nc578618264c24cc0a7121bee79601104
9 Nc93d25d542ec492cb46992d6f6a624dc
10 Ndb52e0a9910846628509eb9c5d62e295
11 Ne2e783678afa4f669c0e3e493f450490
12 Neb2b6e46ca904e1a84d7234fd0291d71
13 Nec11543cff57404f9c8c855e9023b49e
14 Neca02268c96f45ceaf4d5bdc9d37ac20
15 Nfeef79ad72be47b5ba03b97f3fc1dcea
16 anzsrc-for:06
17 anzsrc-for:0604
18 schema:author N82a0c8062af9469eb24475b26bd382d2
19 schema:citation sg:pub.10.1023/a:1011982932645
20 sg:pub.10.1038/nature01012
21 sg:pub.10.1038/nature03959
22 sg:pub.10.1038/ng0102-13
23 sg:pub.10.1038/nrm1648
24 sg:pub.10.1186/1471-2105-2-8
25 sg:pub.10.1186/1471-2164-7-246
26 sg:pub.10.1186/1471-2164-7-272
27 https://doi.org/10.1002/jez.b.21086
28 https://doi.org/10.1016/j.freeradbiomed.2006.08.024
29 https://doi.org/10.1073/pnas.0409169102
30 https://doi.org/10.1093/bioinformatics/bth088
31 https://doi.org/10.1093/emboj/18.19.5399
32 https://doi.org/10.1093/nar/24.1.21
33 https://doi.org/10.1093/nar/29.19.3928
34 https://doi.org/10.1101/gad.11.12.1493
35 https://doi.org/10.1101/gr.1390403
36 https://doi.org/10.1101/gr.2722704
37 https://doi.org/10.1101/gr.4139206
38 https://doi.org/10.1101/gr.5488207
39 https://doi.org/10.1101/gr.6611807
40 https://doi.org/10.1101/gr.6984908
41 https://doi.org/10.1101/gr.8.3.186
42 https://doi.org/10.1101/gr.873003
43 https://doi.org/10.1101/sqb.2003.68.159
44 https://doi.org/10.1101/sqb.2006.71.003
45 https://doi.org/10.1111/j.1365-313x.2007.03244.x
46 https://doi.org/10.1126/science.1061603
47 https://doi.org/10.1261/rna.7135204
48 https://doi.org/10.1895/wormbook.1.1.1
49 schema:datePublished 2008-12
50 schema:datePublishedReg 2008-12-01
51 schema:description BACKGROUND: We have applied a high-throughput pyrosequencing technology for transcriptome profiling of Caenorhabditis elegans in its first larval stage. Using this approach, we have generated a large amount of data for expressed sequence tags, which provides an opportunity for the discovery of putative novel transcripts and alternative splice variants that could be developmentally specific to the first larval stage. This work also demonstrates the successful and efficient application of a next generation sequencing methodology. RESULTS: We have generated over 30 million bases of novel expressed sequence tags from first larval stage worms utilizing high-throughput sequencing technology. We have shown that approximately 14% of the newly sequenced expressed sequence tags map completely or partially to genomic regions where there are no annotated genes or splice variants and therefore, imply that these are novel genetic structures. Expressed sequence tags, which map to intergenic (around 1000) and intronic regions (around 580), may represent novel transcribed regions, such as unannotated or unrecognized small protein-coding or non-protein-coding genes or splice variants. Expressed sequence tags, which map across intron-exon boundaries (around 300), indicate possible alternative splice sites, while expressed sequence tags, which map near the ends of known transcripts (around 600), suggest extension of the coding or untranslated regions. We have also discovered that intergenic and intronic expressed sequence tags, which are well conserved across different nematode species, are likely to represent non-coding RNAs. Lastly, we have incorporated available serial analysis of gene expression data generated from first larval stage worms, in order to predict novel transcripts that might be specifically or predominantly expressed in the first larval stage. CONCLUSION: We have demonstrated the use of a high-throughput sequencing methodology to efficiently produce a snap-shot of transcriptional activities occurring in the first larval stage of C. elegans development. Such application of this new sequencing technique allows for high-throughput, genome-wide experimental verification of known and novel transcripts. This study provides a more complete C. elegans transcriptome profile and, furthermore, gives insight into the evolutionary and biological complexity of this organism.
52 schema:genre research_article
53 schema:inLanguage en
54 schema:isAccessibleForFree true
55 schema:isPartOf N2d60087fc5ef43c88a02df123254ac2f
56 N49b867e7400d40c0b422dbea1005069d
57 sg:journal.1032884
58 schema:name Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags
59 schema:pagination 30
60 schema:productId N3bf6b7c06ee04a99ad6f847148bc94c0
61 N4d276d21ee954fdcab4637183178979f
62 Nb6e12d03a4a74637ad7439b88adc41e2
63 Nb71cdf79fda043f4957afcfdd0fbe616
64 Ne0d72a77af6344dc9615bb9f390e8cc1
65 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048431115
66 https://doi.org/10.1186/1741-7007-6-30
67 schema:sdDatePublished 2019-04-10T20:48
68 schema:sdLicense https://scigraph.springernature.com/explorer/license/
69 schema:sdPublisher N216d3b04f07341dc99e7d0baa9bf3f9c
70 schema:url http://link.springer.com/10.1186%2F1741-7007-6-30
71 sgo:license sg:explorer/license/
72 sgo:sdDataset articles
73 rdf:type schema:ScholarlyArticle
74 N031ebd6e07ca498ebaeb719b56d61715 rdf:first sg:person.01305401161.47
75 rdf:rest N26579b64b22e4fd9bf8827449c2d7d53
76 N21507d85164b4f989af9dd3c60b631be rdf:first sg:person.0601713543.66
77 rdf:rest N724861df5f9d4d25995d8a702b3ef73e
78 N216d3b04f07341dc99e7d0baa9bf3f9c schema:name Springer Nature - SN SciGraph project
79 rdf:type schema:Organization
80 N26579b64b22e4fd9bf8827449c2d7d53 rdf:first sg:person.01150455763.02
81 rdf:rest N2be9c8394eea4dc895da31cb3e14788d
82 N2be9c8394eea4dc895da31cb3e14788d rdf:first sg:person.01315322630.05
83 rdf:rest N6a2ce34b6f2c47f89e3ba6f16f56891d
84 N2d60087fc5ef43c88a02df123254ac2f schema:issueNumber 1
85 rdf:type schema:PublicationIssue
86 N3bf6b7c06ee04a99ad6f847148bc94c0 schema:name doi
87 schema:value 10.1186/1741-7007-6-30
88 rdf:type schema:PropertyValue
89 N49b867e7400d40c0b422dbea1005069d schema:volumeNumber 6
90 rdf:type schema:PublicationVolume
91 N4d276d21ee954fdcab4637183178979f schema:name nlm_unique_id
92 schema:value 101190720
93 rdf:type schema:PropertyValue
94 N556f979411874c0eafb9f86602f3ca59 rdf:first sg:person.01030001224.78
95 rdf:rest N5b2f55be06284983bb6c0e5076b74155
96 N5b2f55be06284983bb6c0e5076b74155 rdf:first sg:person.01023627236.33
97 rdf:rest N031ebd6e07ca498ebaeb719b56d61715
98 N615daf9b345d43499c283b1103672c0b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Caenorhabditis
100 rdf:type schema:DefinedTerm
101 N6a2ce34b6f2c47f89e3ba6f16f56891d rdf:first sg:person.011076371162.80
102 rdf:rest rdf:nil
103 N6d6eeb525b1a4720a3f9111f592debcb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Sequence Analysis, DNA
105 rdf:type schema:DefinedTerm
106 N724861df5f9d4d25995d8a702b3ef73e rdf:first sg:person.01070416716.14
107 rdf:rest N556f979411874c0eafb9f86602f3ca59
108 N82a0c8062af9469eb24475b26bd382d2 rdf:first sg:person.01034505366.45
109 rdf:rest N21507d85164b4f989af9dd3c60b631be
110 N8f3d494297b84d93bf920347547c1390 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Expressed Sequence Tags
112 rdf:type schema:DefinedTerm
113 N926110dcb7cb44a3a960e5bea623c854 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
114 schema:name Animals
115 rdf:type schema:DefinedTerm
116 Nb6e12d03a4a74637ad7439b88adc41e2 schema:name pubmed_id
117 schema:value 18611272
118 rdf:type schema:PropertyValue
119 Nb71cdf79fda043f4957afcfdd0fbe616 schema:name readcube_id
120 schema:value e6b7a4b248d30551efa2b598547dd7a7b9a26e22099360ba47d507f55a85678b
121 rdf:type schema:PropertyValue
122 Nbf62a12794f242ddaeb734981a0f7d56 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name Base Composition
124 rdf:type schema:DefinedTerm
125 Nc1ad2a5752884947a21484ea191d3d17 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
126 schema:name Caenorhabditis elegans
127 rdf:type schema:DefinedTerm
128 Nc3f526986d5c4260a0aa5e5359329795 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Species Specificity
130 rdf:type schema:DefinedTerm
131 Nc578618264c24cc0a7121bee79601104 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
132 schema:name Introns
133 rdf:type schema:DefinedTerm
134 Nc93d25d542ec492cb46992d6f6a624dc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
135 schema:name Genome, Helminth
136 rdf:type schema:DefinedTerm
137 Ndb52e0a9910846628509eb9c5d62e295 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
138 schema:name Protein Isoforms
139 rdf:type schema:DefinedTerm
140 Ne0d72a77af6344dc9615bb9f390e8cc1 schema:name dimensions_id
141 schema:value pub.1048431115
142 rdf:type schema:PropertyValue
143 Ne2e783678afa4f669c0e3e493f450490 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
144 schema:name Exons
145 rdf:type schema:DefinedTerm
146 Neb2b6e46ca904e1a84d7234fd0291d71 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
147 schema:name Larva
148 rdf:type schema:DefinedTerm
149 Nec11543cff57404f9c8c855e9023b49e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
150 schema:name Gene Expression Profiling
151 rdf:type schema:DefinedTerm
152 Neca02268c96f45ceaf4d5bdc9d37ac20 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
153 schema:name Chromosome Mapping
154 rdf:type schema:DefinedTerm
155 Nfeef79ad72be47b5ba03b97f3fc1dcea schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
156 schema:name Conserved Sequence
157 rdf:type schema:DefinedTerm
158 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
159 schema:name Biological Sciences
160 rdf:type schema:DefinedTerm
161 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
162 schema:name Genetics
163 rdf:type schema:DefinedTerm
164 sg:journal.1032884 schema:issn 1478-5854
165 1741-7007
166 schema:name BMC Biology
167 rdf:type schema:Periodical
168 sg:person.01023627236.33 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
169 schema:familyName Mardis
170 schema:givenName Elaine
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023627236.33
172 rdf:type schema:Person
173 sg:person.01030001224.78 schema:affiliation https://www.grid.ac/institutes/grid.4367.6
174 schema:familyName Magrini
175 schema:givenName Vincent
176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030001224.78
177 rdf:type schema:Person
178 sg:person.01034505366.45 schema:affiliation https://www.grid.ac/institutes/grid.248762.d
179 schema:familyName Shin
180 schema:givenName Heesun
181 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01034505366.45
182 rdf:type schema:Person
183 sg:person.01070416716.14 schema:affiliation https://www.grid.ac/institutes/grid.248762.d
184 schema:familyName Bainbridge
185 schema:givenName Matthew N
186 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070416716.14
187 rdf:type schema:Person
188 sg:person.011076371162.80 schema:affiliation https://www.grid.ac/institutes/grid.248762.d
189 schema:familyName Jones
190 schema:givenName Steven JM
191 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011076371162.80
192 rdf:type schema:Person
193 sg:person.01150455763.02 schema:affiliation https://www.grid.ac/institutes/grid.248762.d
194 schema:familyName Marra
195 schema:givenName Marco A
196 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01150455763.02
197 rdf:type schema:Person
198 sg:person.01305401161.47 schema:affiliation https://www.grid.ac/institutes/grid.17091.3e
199 schema:familyName Moerman
200 schema:givenName Donald G
201 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305401161.47
202 rdf:type schema:Person
203 sg:person.01315322630.05 schema:affiliation https://www.grid.ac/institutes/grid.61971.38
204 schema:familyName Baillie
205 schema:givenName David L
206 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315322630.05
207 rdf:type schema:Person
208 sg:person.0601713543.66 schema:affiliation https://www.grid.ac/institutes/grid.248762.d
209 schema:familyName Hirst
210 schema:givenName Martin
211 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601713543.66
212 rdf:type schema:Person
213 sg:pub.10.1023/a:1011982932645 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011731095
214 https://doi.org/10.1023/a:1011982932645
215 rdf:type schema:CreativeWork
216 sg:pub.10.1038/nature01012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046557993
217 https://doi.org/10.1038/nature01012
218 rdf:type schema:CreativeWork
219 sg:pub.10.1038/nature03959 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021574562
220 https://doi.org/10.1038/nature03959
221 rdf:type schema:CreativeWork
222 sg:pub.10.1038/ng0102-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025102244
223 https://doi.org/10.1038/ng0102-13
224 rdf:type schema:CreativeWork
225 sg:pub.10.1038/nrm1648 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003259347
226 https://doi.org/10.1038/nrm1648
227 rdf:type schema:CreativeWork
228 sg:pub.10.1186/1471-2105-2-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046362248
229 https://doi.org/10.1186/1471-2105-2-8
230 rdf:type schema:CreativeWork
231 sg:pub.10.1186/1471-2164-7-246 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026547515
232 https://doi.org/10.1186/1471-2164-7-246
233 rdf:type schema:CreativeWork
234 sg:pub.10.1186/1471-2164-7-272 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040475066
235 https://doi.org/10.1186/1471-2164-7-272
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1002/jez.b.21086 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007388294
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1016/j.freeradbiomed.2006.08.024 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036491564
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1073/pnas.0409169102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016701541
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1093/bioinformatics/bth088 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022171874
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1093/emboj/18.19.5399 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005082025
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1093/nar/24.1.21 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013074371
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1093/nar/29.19.3928 schema:sameAs https://app.dimensions.ai/details/publication/pub.1074886589
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1101/gad.11.12.1493 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001434602
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1101/gr.1390403 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014635681
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1101/gr.2722704 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024280946
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1101/gr.4139206 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004882909
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1101/gr.5488207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048766691
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1101/gr.6611807 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047705066
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1101/gr.6984908 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010761083
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1101/gr.8.3.186 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038920266
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1101/gr.873003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002115475
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1101/sqb.2003.68.159 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060415953
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1101/sqb.2006.71.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013387185
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1111/j.1365-313x.2007.03244.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1028076986
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1126/science.1061603 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062445115
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1261/rna.7135204 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023833580
278 rdf:type schema:CreativeWork
279 https://doi.org/10.1895/wormbook.1.1.1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1068724073
280 rdf:type schema:CreativeWork
281 https://www.grid.ac/institutes/grid.17091.3e schema:alternateName University of British Columbia
282 schema:name Department of Zoology, University of British Columbia, Vancouver, BC, Canada
283 rdf:type schema:Organization
284 https://www.grid.ac/institutes/grid.248762.d schema:alternateName BC Cancer Agency
285 schema:name Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
286 Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
287 rdf:type schema:Organization
288 https://www.grid.ac/institutes/grid.4367.6 schema:alternateName Washington University in St. Louis
289 schema:name Genome Sequencing Center, Washington University School of Medicine, St Louis, USA
290 rdf:type schema:Organization
291 https://www.grid.ac/institutes/grid.61971.38 schema:alternateName Simon Fraser University
292 schema:name Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
293 rdf:type schema:Organization
 




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


...