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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-07-08

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/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "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"
      }, 
      {
        "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": "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada", 
          "id": "http://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": "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada", 
          "id": "http://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": "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada", 
          "id": "http://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": "Genome Sequencing Center, Washington University School of Medicine, St Louis, USA", 
          "id": "http://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": "Genome Sequencing Center, Washington University School of Medicine, St Louis, USA", 
          "id": "http://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": "Department of Zoology, University of British Columbia, Vancouver, BC, Canada", 
          "id": "http://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": "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada", 
          "id": "http://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": "Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada", 
          "id": "http://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": "Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada", 
          "id": "http://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": "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.10.1038/nrm1648", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003259347", 
          "https://doi.org/10.1038/nrm1648"
        ], 
        "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/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": "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": "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/nature01012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046557993", 
          "https://doi.org/10.1038/nature01012"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-07-08", 
    "datePublishedReg": "2008-07-08", 
    "description": "Abstract\nBackground\nWe 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\nWe 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\nWe 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": "article", 
    "id": "sg:pub.10.1186/1741-7007-6-30", 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1032884", 
        "issn": [
          "1478-5854", 
          "1741-7007"
        ], 
        "name": "BMC Biology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "6"
      }
    ], 
    "keywords": [
      "first larval stage", 
      "sequence tags", 
      "novel transcripts", 
      "larval stages", 
      "splice variants", 
      "high-throughput sequencing methodologies", 
      "sequencing methodologies", 
      "high-throughput sequencing technology", 
      "C. elegans development", 
      "putative novel transcripts", 
      "high-throughput pyrosequencing technology", 
      "different nematode species", 
      "non-coding RNAs", 
      "next-generation sequencing methodologies", 
      "alternative splice sites", 
      "stage worms", 
      "novel genetic structure", 
      "alternative splice variants", 
      "gene expression data", 
      "new sequencing techniques", 
      "intron-exon boundaries", 
      "genetic structure", 
      "genomic regions", 
      "transcriptome profiling", 
      "transcriptome profiles", 
      "nematode species", 
      "sequencing technologies", 
      "transcriptional activity", 
      "untranslated region", 
      "intronic regions", 
      "sequencing techniques", 
      "expression data", 
      "splice site", 
      "biological complexity", 
      "basis of novel", 
      "serial analysis", 
      "transcripts", 
      "pyrosequencing technology", 
      "Caenorhabditis", 
      "genes", 
      "tags", 
      "variants", 
      "worms", 
      "intergenic", 
      "RNA", 
      "organisms", 
      "species", 
      "profiling", 
      "region", 
      "stage", 
      "discovery", 
      "sites", 
      "insights", 
      "large amount", 
      "activity", 
      "analysis", 
      "novel", 
      "development", 
      "basis", 
      "structure", 
      "profile", 
      "efficient application", 
      "data", 
      "amount", 
      "study", 
      "end", 
      "results", 
      "complexity", 
      "opportunities", 
      "background", 
      "technology", 
      "approach", 
      "applications", 
      "use", 
      "conclusion", 
      "extension", 
      "order", 
      "work", 
      "boundaries", 
      "coding", 
      "methodology", 
      "technique", 
      "experimental verification", 
      "such applications", 
      "verification"
    ], 
    "name": "Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags", 
    "pagination": "30", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1048431115"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1741-7007-6-30"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18611272"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1741-7007-6-30", 
      "https://app.dimensions.ai/details/publication/pub.1048431115"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-11-24T20:53", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221124/entities/gbq_results/article/article_463.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1741-7007-6-30"
  }
]
 

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.

304 TRIPLES      21 PREDICATES      133 URIs      117 LITERALS      22 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1741-7007-6-30 schema:about N00900b728bff464e8b402849830e5516
2 N0149e79652754fc5b7571c7ea74e1b04
3 N11bf9073fa1a4d56a1929c08c3855419
4 N193c06430cad4217ade2875a57f7541d
5 N1e8005c7fadc45318b8a31f9aa085fe6
6 N286b47fc62704184a433d984db44a49b
7 N2f47b2b37a3f4fb49bbc8abe73fe3566
8 N3184b47e5f254bafbc5281a366d508e4
9 N35f054e495684f66ba2163d95a9ea491
10 N39f8645f37a646fbab356d6fd1f4a34e
11 N3dec5b2173aa4cb5ba2e18825512c985
12 N3f1d8b3b9dc74a9da2afdfc7386628e4
13 Nac4e527e20424920b50fa42b40e6d51b
14 Nd2bd9db501e64b0e9f29d7216bbebed8
15 Nd4511169785d4ef884b8aaac958181e5
16 anzsrc-for:06
17 anzsrc-for:0604
18 schema:author Nd618036ac55742c6ba550d202c5d386a
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 schema:datePublished 2008-07-08
28 schema:datePublishedReg 2008-07-08
29 schema:description 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.
30 schema:genre article
31 schema:isAccessibleForFree true
32 schema:isPartOf N70030ecb38634fc0b628690b013be814
33 Nc3385338c93a41e19362552f9e23077e
34 sg:journal.1032884
35 schema:keywords C. elegans development
36 Caenorhabditis
37 RNA
38 activity
39 alternative splice sites
40 alternative splice variants
41 amount
42 analysis
43 applications
44 approach
45 background
46 basis
47 basis of novel
48 biological complexity
49 boundaries
50 coding
51 complexity
52 conclusion
53 data
54 development
55 different nematode species
56 discovery
57 efficient application
58 end
59 experimental verification
60 expression data
61 extension
62 first larval stage
63 gene expression data
64 genes
65 genetic structure
66 genomic regions
67 high-throughput pyrosequencing technology
68 high-throughput sequencing methodologies
69 high-throughput sequencing technology
70 insights
71 intergenic
72 intron-exon boundaries
73 intronic regions
74 large amount
75 larval stages
76 methodology
77 nematode species
78 new sequencing techniques
79 next-generation sequencing methodologies
80 non-coding RNAs
81 novel
82 novel genetic structure
83 novel transcripts
84 opportunities
85 order
86 organisms
87 profile
88 profiling
89 putative novel transcripts
90 pyrosequencing technology
91 region
92 results
93 sequence tags
94 sequencing methodologies
95 sequencing techniques
96 sequencing technologies
97 serial analysis
98 sites
99 species
100 splice site
101 splice variants
102 stage
103 stage worms
104 structure
105 study
106 such applications
107 tags
108 technique
109 technology
110 transcriptional activity
111 transcriptome profiles
112 transcriptome profiling
113 transcripts
114 untranslated region
115 use
116 variants
117 verification
118 work
119 worms
120 schema:name Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags
121 schema:pagination 30
122 schema:productId N20d219039de1415db89a8aa2470d5e5e
123 N5e301ceab9ba411ab74283001176dfd5
124 Nc49f9d75dd474002a86eda765e0823ae
125 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048431115
126 https://doi.org/10.1186/1741-7007-6-30
127 schema:sdDatePublished 2022-11-24T20:53
128 schema:sdLicense https://scigraph.springernature.com/explorer/license/
129 schema:sdPublisher N537da681c6e3455f80d7f2fdd07bdf87
130 schema:url https://doi.org/10.1186/1741-7007-6-30
131 sgo:license sg:explorer/license/
132 sgo:sdDataset articles
133 rdf:type schema:ScholarlyArticle
134 N00900b728bff464e8b402849830e5516 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
135 schema:name Protein Isoforms
136 rdf:type schema:DefinedTerm
137 N0149e79652754fc5b7571c7ea74e1b04 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
138 schema:name Genome, Helminth
139 rdf:type schema:DefinedTerm
140 N0e91064d0b9c48838b2d8ebc5cbdfe24 rdf:first sg:person.01023627236.33
141 rdf:rest N5b8776c6a908488d9629a4350b6a6f7d
142 N11bf9073fa1a4d56a1929c08c3855419 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
143 schema:name Larva
144 rdf:type schema:DefinedTerm
145 N12554bbd65284304b191f9e7ff942b1e rdf:first sg:person.01070416716.14
146 rdf:rest N6a7c1a98dba343e99f67506758b6e382
147 N193c06430cad4217ade2875a57f7541d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name Caenorhabditis
149 rdf:type schema:DefinedTerm
150 N1e8005c7fadc45318b8a31f9aa085fe6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
151 schema:name Gene Expression Profiling
152 rdf:type schema:DefinedTerm
153 N20d219039de1415db89a8aa2470d5e5e schema:name doi
154 schema:value 10.1186/1741-7007-6-30
155 rdf:type schema:PropertyValue
156 N286b47fc62704184a433d984db44a49b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
157 schema:name Caenorhabditis elegans
158 rdf:type schema:DefinedTerm
159 N2f47b2b37a3f4fb49bbc8abe73fe3566 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
160 schema:name Chromosome Mapping
161 rdf:type schema:DefinedTerm
162 N3184b47e5f254bafbc5281a366d508e4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
163 schema:name Expressed Sequence Tags
164 rdf:type schema:DefinedTerm
165 N35f054e495684f66ba2163d95a9ea491 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
166 schema:name Animals
167 rdf:type schema:DefinedTerm
168 N39f8645f37a646fbab356d6fd1f4a34e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
169 schema:name Exons
170 rdf:type schema:DefinedTerm
171 N3dec5b2173aa4cb5ba2e18825512c985 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
172 schema:name Species Specificity
173 rdf:type schema:DefinedTerm
174 N3f1d8b3b9dc74a9da2afdfc7386628e4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
175 schema:name Sequence Analysis, DNA
176 rdf:type schema:DefinedTerm
177 N4039afd606284163b354bef5c87b9e05 rdf:first sg:person.01315322630.05
178 rdf:rest Nc9418cba0da248f8a25bb59ddf02d6c3
179 N537da681c6e3455f80d7f2fdd07bdf87 schema:name Springer Nature - SN SciGraph project
180 rdf:type schema:Organization
181 N56783ae41e0e41409f8df1cdf8242312 rdf:first sg:person.01150455763.02
182 rdf:rest N4039afd606284163b354bef5c87b9e05
183 N5b8776c6a908488d9629a4350b6a6f7d rdf:first sg:person.01305401161.47
184 rdf:rest N56783ae41e0e41409f8df1cdf8242312
185 N5e301ceab9ba411ab74283001176dfd5 schema:name pubmed_id
186 schema:value 18611272
187 rdf:type schema:PropertyValue
188 N6a7c1a98dba343e99f67506758b6e382 rdf:first sg:person.01030001224.78
189 rdf:rest N0e91064d0b9c48838b2d8ebc5cbdfe24
190 N6d0a767f5bb746b7a383da3a0cee3135 rdf:first sg:person.0601713543.66
191 rdf:rest N12554bbd65284304b191f9e7ff942b1e
192 N70030ecb38634fc0b628690b013be814 schema:volumeNumber 6
193 rdf:type schema:PublicationVolume
194 Nac4e527e20424920b50fa42b40e6d51b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
195 schema:name Conserved Sequence
196 rdf:type schema:DefinedTerm
197 Nc3385338c93a41e19362552f9e23077e schema:issueNumber 1
198 rdf:type schema:PublicationIssue
199 Nc49f9d75dd474002a86eda765e0823ae schema:name dimensions_id
200 schema:value pub.1048431115
201 rdf:type schema:PropertyValue
202 Nc9418cba0da248f8a25bb59ddf02d6c3 rdf:first sg:person.011076371162.80
203 rdf:rest rdf:nil
204 Nd2bd9db501e64b0e9f29d7216bbebed8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
205 schema:name Base Composition
206 rdf:type schema:DefinedTerm
207 Nd4511169785d4ef884b8aaac958181e5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
208 schema:name Introns
209 rdf:type schema:DefinedTerm
210 Nd618036ac55742c6ba550d202c5d386a rdf:first sg:person.01034505366.45
211 rdf:rest N6d0a767f5bb746b7a383da3a0cee3135
212 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
213 schema:name Biological Sciences
214 rdf:type schema:DefinedTerm
215 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
216 schema:name Genetics
217 rdf:type schema:DefinedTerm
218 sg:journal.1032884 schema:issn 1478-5854
219 1741-7007
220 schema:name BMC Biology
221 schema:publisher Springer Nature
222 rdf:type schema:Periodical
223 sg:person.01023627236.33 schema:affiliation grid-institutes:grid.4367.6
224 schema:familyName Mardis
225 schema:givenName Elaine
226 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023627236.33
227 rdf:type schema:Person
228 sg:person.01030001224.78 schema:affiliation grid-institutes:grid.4367.6
229 schema:familyName Magrini
230 schema:givenName Vincent
231 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030001224.78
232 rdf:type schema:Person
233 sg:person.01034505366.45 schema:affiliation grid-institutes:grid.248762.d
234 schema:familyName Shin
235 schema:givenName Heesun
236 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01034505366.45
237 rdf:type schema:Person
238 sg:person.01070416716.14 schema:affiliation grid-institutes:grid.248762.d
239 schema:familyName Bainbridge
240 schema:givenName Matthew N
241 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070416716.14
242 rdf:type schema:Person
243 sg:person.011076371162.80 schema:affiliation grid-institutes:grid.248762.d
244 schema:familyName Jones
245 schema:givenName Steven JM
246 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011076371162.80
247 rdf:type schema:Person
248 sg:person.01150455763.02 schema:affiliation grid-institutes:grid.248762.d
249 schema:familyName Marra
250 schema:givenName Marco A
251 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01150455763.02
252 rdf:type schema:Person
253 sg:person.01305401161.47 schema:affiliation grid-institutes:grid.17091.3e
254 schema:familyName Moerman
255 schema:givenName Donald G
256 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305401161.47
257 rdf:type schema:Person
258 sg:person.01315322630.05 schema:affiliation grid-institutes:grid.61971.38
259 schema:familyName Baillie
260 schema:givenName David L
261 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315322630.05
262 rdf:type schema:Person
263 sg:person.0601713543.66 schema:affiliation grid-institutes:grid.248762.d
264 schema:familyName Hirst
265 schema:givenName Martin
266 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601713543.66
267 rdf:type schema:Person
268 sg:pub.10.1023/a:1011982932645 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011731095
269 https://doi.org/10.1023/a:1011982932645
270 rdf:type schema:CreativeWork
271 sg:pub.10.1038/nature01012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046557993
272 https://doi.org/10.1038/nature01012
273 rdf:type schema:CreativeWork
274 sg:pub.10.1038/nature03959 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021574562
275 https://doi.org/10.1038/nature03959
276 rdf:type schema:CreativeWork
277 sg:pub.10.1038/ng0102-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025102244
278 https://doi.org/10.1038/ng0102-13
279 rdf:type schema:CreativeWork
280 sg:pub.10.1038/nrm1648 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003259347
281 https://doi.org/10.1038/nrm1648
282 rdf:type schema:CreativeWork
283 sg:pub.10.1186/1471-2105-2-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046362248
284 https://doi.org/10.1186/1471-2105-2-8
285 rdf:type schema:CreativeWork
286 sg:pub.10.1186/1471-2164-7-246 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026547515
287 https://doi.org/10.1186/1471-2164-7-246
288 rdf:type schema:CreativeWork
289 sg:pub.10.1186/1471-2164-7-272 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040475066
290 https://doi.org/10.1186/1471-2164-7-272
291 rdf:type schema:CreativeWork
292 grid-institutes:grid.17091.3e schema:alternateName Department of Zoology, University of British Columbia, Vancouver, BC, Canada
293 schema:name Department of Zoology, University of British Columbia, Vancouver, BC, Canada
294 rdf:type schema:Organization
295 grid-institutes:grid.248762.d schema:alternateName Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
296 schema:name Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
297 Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
298 rdf:type schema:Organization
299 grid-institutes:grid.4367.6 schema:alternateName Genome Sequencing Center, Washington University School of Medicine, St Louis, USA
300 schema:name Genome Sequencing Center, Washington University School of Medicine, St Louis, USA
301 rdf:type schema:Organization
302 grid-institutes:grid.61971.38 schema:alternateName Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
303 schema:name Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
304 rdf:type schema:Organization
 




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


...