Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-05-02

AUTHORS

Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter

ABSTRACT

RNA-Seq enables rapid sequencing of total cellular RNA and should allow the reconstruction of spliced transcripts in a cell population. Trapnell et al. achieve this and transcript quantification using only paired-end RNA-Seq data and an unannotated genome sequence, and apply the approach to characterize isoform switching over a developmental time course. More... »

PAGES

511-515

Journal

TITLE

Nature Biotechnology

ISSUE

5

VOLUME

28

Related Patents

  • Systems And Methods For Preventing, Mitigating, And/Or Treating Dementia
  • Methods For Treating Cells Containing Fusion Genes
  • Fusion Genes Associated With Progressive Prostate Cancer
  • Column-Based Device And Method For Retrieval Of Rare Cells Based On Size, And Uses Thereof
  • Compositions And Methods For Treating Patients Suffering From Glioma Or Leukemia
  • Systems And Methods For Genomic Pattern Analysis
  • Esophageal Microrna Expression Profiles In Eosinophilic Esophagitis
  • Methods, Apparatuses, And Systems For Analyzing Microorganism Strains From Complex Heterogeneous Communities, Predicting And Identifying Functional Relationships And Interactions Thereof, And Selecting And Synthesizing Microbial Ensembles Based Thereon
  • Method And System For Quantifying Sequence Alignment
  • Alteration Of Neuronal Gene Expression By Synthetic Pirnas And By Alteration Of Pirna Function
  • Methods For Controlled Identification And/Or Quantification Of Transcript Variants In One Or More Samples
  • Materials And Methods For The Treatment Of Vascular Disease
  • Methods For Programming Differentiated Cells Into Hematopoietic Stem Cells
  • Methods For Identifying Androgen Receptor Splice Variants In Subjects Having Castration Resistant Prostate Cancer
  • Systems And Methods For Using Paired-End Data In Directed Acyclic Structure
  • Means And Methods For Determining T Cell Recognition
  • Methods Of Treating Cells Containing Fusion Genes
  • Methods For Treating Cells Containing Fusion Genes
  • Fusion Genes Associated With Progressive Prostate Cancer
  • Fusion Genes Associated With Progressive Prostate Cancer
  • Ddx43 As A Biomarker Of Resistance To Mek1/2 Inhibitors
  • Methods And Systems For Detecting Sequence Variants
  • Systems And Methods For Smart Tools In Sequence Pipelines
  • Esophageal Microrna Expression Profiles In Eosinophilic Esophagitis
  • Trna Derived Small Rnas (Tsrnas) Involved In Cell Viability
  • Personalized Myeloma Detection
  • Sex Determination Genes And Their Use In Breeding
  • Methods And Systems For Detecting Sequence Variants
  • Transcript Determination Method
  • Methods, Apparatuses, And Systems For Microorganism Strain Analysis Of Complex Heterogeneous Communities, Predicting And Identifying Functional Relationships And Interactions Thereof, And Selecting And Synthesizing Microbial Ensembles Based Thereon
  • Transcript Determination Method
  • Systems And Methods For Preventing, Mitigating, And/Or Treating Dementia
  • Generation Of Functional And Durable Endothelial Cells From Human Amniotic Fluid-Derived Cells
  • Materials And Methods For The Treatment Of Vascular Disease
  • Means And Methods For Determining T Cell Recognition
  • Systems And Methods For Analyzing Sequence Data
  • Methods Of Isolating T Cells And T Cell Receptors Having Antigenic Specificity For A Cancer-Specific Mutation From Peripheral Blood
  • In Silico Design Of Mammalian Promoters With User-Defined Functionality
  • Methods And Systems For Converting Precursor Cells Into Intestinal Tissues Through Directed Differentiation
  • Ezh2 Inhibitor-Induced Gene Expression
  • Compositions And Methods For Increasing Salt Tolerance In Plants
  • Methods, Apparatuses And Systems For Analyzing Microorganism Strains From Complex Heterogeneous Communities, Predicting And Identifying Functional Relationships And Interactions Thereof, And Selecting And Synthesizing Microbial Ensembles Based Thereon
  • Medical Uses, Methods And Uses
  • Methods And Devices For Providing A Stimulus To A Subject To Induce Gamma Oscillations
  • Induction Of Myelinating Oligodendrocytes In Human Cortical Spheroids
  • New Peptide Derivatives Of Platelet Derived Growth Factor (Pdgf), A Method For Their Preparation, Pharmaceutical Compositions Containing Them And Application Of These Compositions
  • Fusion Genes Associated With Progressive Prostate Cancer
  • Fusion Genes Associated With Progressive Prostate Cancer
  • Ddx43 As A Biomarker Of Resistance To Mek1/2 Inhibitors
  • Systems And Methods For Treating Dementia
  • Targeting Chromosomal Instability And Downstream Cytosolic Dna Signaling For Cancer Treatment
  • Methods And Systems For Aligning Sequences
  • Nucleic Acid Transcription Method
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nbt.1621

    DOI

    http://dx.doi.org/10.1038/nbt.1621

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1031035095

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20436464


    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": "Algorithms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Cell Differentiation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Cell Line", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Profiling", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mice", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Oligonucleotide Array Sequence Analysis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Isoforms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Proto-Oncogene Proteins c-myc", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Messenger", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, RNA", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Software", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Mathematics, University of California, Berkeley, California, USA", 
              "id": "http://www.grid.ac/institutes/grid.47840.3f", 
              "name": [
                "Department of Computer Science, University of Maryland, College Park, Maryland, USA", 
                "Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA", 
                "Department of Mathematics, University of California, Berkeley, California, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Trapnell", 
            "givenName": "Cole", 
            "id": "sg:person.01247375013.30", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247375013.30"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA", 
              "id": "http://www.grid.ac/institutes/grid.20861.3d", 
              "name": [
                "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Williams", 
            "givenName": "Brian A", 
            "id": "sg:person.0741140331.06", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741140331.06"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA", 
              "id": "http://www.grid.ac/institutes/grid.164295.d", 
              "name": [
                "Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pertea", 
            "givenName": "Geo", 
            "id": "sg:person.01024612415.46", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024612415.46"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA", 
              "id": "http://www.grid.ac/institutes/grid.20861.3d", 
              "name": [
                "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mortazavi", 
            "givenName": "Ali", 
            "id": "sg:person.0673025131.06", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0673025131.06"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA", 
              "id": "http://www.grid.ac/institutes/grid.20861.3d", 
              "name": [
                "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kwan", 
            "givenName": "Gordon", 
            "id": "sg:person.0774300251.64", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774300251.64"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Genome Sciences Center, Washington University in St. Louis, St. Louis, Missouri, USA", 
              "id": "http://www.grid.ac/institutes/grid.4367.6", 
              "name": [
                "Genome Sciences Center, Washington University in St. Louis, St. Louis, Missouri, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "van Baren", 
            "givenName": "Marijke J", 
            "id": "sg:person.01042023041.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042023041.45"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA", 
              "id": "http://www.grid.ac/institutes/grid.164295.d", 
              "name": [
                "Department of Computer Science, University of Maryland, College Park, Maryland, USA", 
                "Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Salzberg", 
            "givenName": "Steven L", 
            "id": "sg:person.01223441713.02", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223441713.02"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA", 
              "id": "http://www.grid.ac/institutes/grid.20861.3d", 
              "name": [
                "Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wold", 
            "givenName": "Barbara J", 
            "id": "sg:person.01026162263.73", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01026162263.73"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Computer Science, University of California, Berkeley, California, USA", 
              "id": "http://www.grid.ac/institutes/grid.47840.3f", 
              "name": [
                "Department of Mathematics, University of California, Berkeley, California, USA", 
                "Department of Molecular and Cell Biology, University of California, Berkeley, California, USA", 
                "Department of Computer Science, University of California, Berkeley, California, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pachter", 
            "givenName": "Lior", 
            "id": "sg:person.0672165566.75", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0672165566.75"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nature07509", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029002744", 
              "https://doi.org/10.1038/nature07509"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-11-94", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053091615", 
              "https://doi.org/10.1186/1471-2105-11-94"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07672", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051133532", 
              "https://doi.org/10.1038/nature07672"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08195", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007963177", 
              "https://doi.org/10.1038/nature08195"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1226", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045381177", 
              "https://doi.org/10.1038/nmeth.1226"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07638", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009442631", 
              "https://doi.org/10.1038/nature07638"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1371", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011651858", 
              "https://doi.org/10.1038/nmeth.1371"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2008-9-12-r175", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016469219", 
              "https://doi.org/10.1186/gb-2008-9-12-r175"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2009-10-3-r25", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049583368", 
              "https://doi.org/10.1186/gb-2009-10-3-r25"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1223", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048586936", 
              "https://doi.org/10.1038/nmeth.1223"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature05676", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030633547", 
              "https://doi.org/10.1038/nature05676"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2010-05-02", 
        "datePublishedReg": "2010-05-02", 
        "description": "RNA-Seq enables rapid sequencing of total cellular RNA and should allow the reconstruction of spliced transcripts in a cell population. Trapnell et al. achieve this and transcript quantification using only paired-end RNA-Seq data and an unannotated genome sequence, and apply the approach to characterize isoform switching over a developmental time course.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/nbt.1621", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2699343", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2545461", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2529425", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2519905", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1115214", 
            "issn": [
              "1087-0156", 
              "1546-1696"
            ], 
            "name": "Nature Biotechnology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "5", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "28"
          }
        ], 
        "keywords": [
          "RNA-seq", 
          "unannotated genome sequence", 
          "RNA-seq data", 
          "total cellular RNA", 
          "paired-end RNA-seq data", 
          "unannotated transcripts", 
          "genome sequence", 
          "transcript assembly", 
          "spliced transcripts", 
          "cellular RNA", 
          "cell differentiation", 
          "transcript quantification", 
          "rapid sequencing", 
          "cell populations", 
          "developmental time course", 
          "transcripts", 
          "RNA", 
          "sequencing", 
          "isoforms", 
          "differentiation", 
          "sequence", 
          "assembly", 
          "time course", 
          "population", 
          "quantification", 
          "data", 
          "approach", 
          "reconstruction", 
          "course"
        ], 
        "name": "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation", 
        "pagination": "511-515", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1031035095"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/nbt.1621"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "20436464"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/nbt.1621", 
          "https://app.dimensions.ai/details/publication/pub.1031035095"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-05-20T07:26", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220519/entities/gbq_results/article/article_521.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/nbt.1621"
      }
    ]
     

    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/nbt.1621'

    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/nbt.1621'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.1621'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt.1621'


     

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

    266 TRIPLES      22 PREDICATES      79 URIs      60 LITERALS      20 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/nbt.1621 schema:about N01eb150d76934bc7b7f4ec71194ad2ec
    2 N0bf6ffb603b44399908efb30acec335c
    3 N1b638f94001944378bddef527966145a
    4 N303e182519ec4071b95b1dce040d4e9d
    5 N370b42a59d994643abc72fa581c1404b
    6 N3896844e994c4f4b9446f9981eab7ca3
    7 N7676e3c87c144cc0be9c3556cac88f8c
    8 N92ab1fd6801c430eb532664e200b8fff
    9 N9e6a92aff53e4e08bf0b793ab3d8f8c5
    10 Nab9f70c21d684f528cc81ffb5e20c9f8
    11 Nc0f667a01a484b65acab99f1e6912566
    12 Ndda0a6b098ea45feb49a4ecf2d2278e4
    13 Nfb545a9845d247339a23ebf9e6788a66
    14 anzsrc-for:06
    15 anzsrc-for:0604
    16 schema:author N38a93f4df4b249969d3fe8231290200e
    17 schema:citation sg:pub.10.1038/nature05676
    18 sg:pub.10.1038/nature07509
    19 sg:pub.10.1038/nature07638
    20 sg:pub.10.1038/nature07672
    21 sg:pub.10.1038/nature08195
    22 sg:pub.10.1038/nmeth.1223
    23 sg:pub.10.1038/nmeth.1226
    24 sg:pub.10.1038/nmeth.1371
    25 sg:pub.10.1186/1471-2105-11-94
    26 sg:pub.10.1186/gb-2008-9-12-r175
    27 sg:pub.10.1186/gb-2009-10-3-r25
    28 schema:datePublished 2010-05-02
    29 schema:datePublishedReg 2010-05-02
    30 schema:description RNA-Seq enables rapid sequencing of total cellular RNA and should allow the reconstruction of spliced transcripts in a cell population. Trapnell et al. achieve this and transcript quantification using only paired-end RNA-Seq data and an unannotated genome sequence, and apply the approach to characterize isoform switching over a developmental time course.
    31 schema:genre article
    32 schema:inLanguage en
    33 schema:isAccessibleForFree true
    34 schema:isPartOf Nc620ff7a5544418da43e6abc47469c57
    35 Ne6a1245f092e45af8a65dda4c558d3e9
    36 sg:journal.1115214
    37 schema:keywords RNA
    38 RNA-seq
    39 RNA-seq data
    40 approach
    41 assembly
    42 cell differentiation
    43 cell populations
    44 cellular RNA
    45 course
    46 data
    47 developmental time course
    48 differentiation
    49 genome sequence
    50 isoforms
    51 paired-end RNA-seq data
    52 population
    53 quantification
    54 rapid sequencing
    55 reconstruction
    56 sequence
    57 sequencing
    58 spliced transcripts
    59 time course
    60 total cellular RNA
    61 transcript assembly
    62 transcript quantification
    63 transcripts
    64 unannotated genome sequence
    65 unannotated transcripts
    66 schema:name Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    67 schema:pagination 511-515
    68 schema:productId N05042de9e0814f8485d5db1ad3ec488e
    69 N9e5adaade8c64ad897390261c51c54bb
    70 Nea6cf4f52f9a4db1bf4810d3c75dd25a
    71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031035095
    72 https://doi.org/10.1038/nbt.1621
    73 schema:sdDatePublished 2022-05-20T07:26
    74 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    75 schema:sdPublisher N178091746d2d4aceaa7774b86012f977
    76 schema:url https://doi.org/10.1038/nbt.1621
    77 sgo:license sg:explorer/license/
    78 sgo:sdDataset articles
    79 rdf:type schema:ScholarlyArticle
    80 N01eb150d76934bc7b7f4ec71194ad2ec schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    81 schema:name Algorithms
    82 rdf:type schema:DefinedTerm
    83 N05042de9e0814f8485d5db1ad3ec488e schema:name dimensions_id
    84 schema:value pub.1031035095
    85 rdf:type schema:PropertyValue
    86 N0bf6ffb603b44399908efb30acec335c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    87 schema:name RNA, Messenger
    88 rdf:type schema:DefinedTerm
    89 N178091746d2d4aceaa7774b86012f977 schema:name Springer Nature - SN SciGraph project
    90 rdf:type schema:Organization
    91 N1b638f94001944378bddef527966145a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    92 schema:name Oligonucleotide Array Sequence Analysis
    93 rdf:type schema:DefinedTerm
    94 N293c7b4f50d84f5c9fa86347dee0d34c rdf:first sg:person.0741140331.06
    95 rdf:rest N6c2e9fcca08249a5b9ebfe3d89154c03
    96 N303e182519ec4071b95b1dce040d4e9d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    97 schema:name Cell Differentiation
    98 rdf:type schema:DefinedTerm
    99 N370b42a59d994643abc72fa581c1404b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    100 schema:name Sequence Analysis, RNA
    101 rdf:type schema:DefinedTerm
    102 N3896844e994c4f4b9446f9981eab7ca3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    103 schema:name Mice
    104 rdf:type schema:DefinedTerm
    105 N38a93f4df4b249969d3fe8231290200e rdf:first sg:person.01247375013.30
    106 rdf:rest N293c7b4f50d84f5c9fa86347dee0d34c
    107 N6c2e9fcca08249a5b9ebfe3d89154c03 rdf:first sg:person.01024612415.46
    108 rdf:rest N81b77e7544f2408fa32d235951255a83
    109 N7676e3c87c144cc0be9c3556cac88f8c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    110 schema:name Cell Line
    111 rdf:type schema:DefinedTerm
    112 N7d9ed559beca4dfa89cb6c4c6a1063b2 rdf:first sg:person.01042023041.45
    113 rdf:rest Nc53283300dbf457ba9044da5401d952c
    114 N81b77e7544f2408fa32d235951255a83 rdf:first sg:person.0673025131.06
    115 rdf:rest Nd4dee59428ce445682537f6309b18995
    116 N85535fddda124f94b60ed868a6b4a705 rdf:first sg:person.0672165566.75
    117 rdf:rest rdf:nil
    118 N92ab1fd6801c430eb532664e200b8fff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    119 schema:name Software
    120 rdf:type schema:DefinedTerm
    121 N9e5adaade8c64ad897390261c51c54bb schema:name pubmed_id
    122 schema:value 20436464
    123 rdf:type schema:PropertyValue
    124 N9e6a92aff53e4e08bf0b793ab3d8f8c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    125 schema:name Genome
    126 rdf:type schema:DefinedTerm
    127 Nab9f70c21d684f528cc81ffb5e20c9f8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    128 schema:name Gene Expression Profiling
    129 rdf:type schema:DefinedTerm
    130 Nb011d02c8afb4aa2938633029ba012e3 rdf:first sg:person.01026162263.73
    131 rdf:rest N85535fddda124f94b60ed868a6b4a705
    132 Nc0f667a01a484b65acab99f1e6912566 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    133 schema:name Animals
    134 rdf:type schema:DefinedTerm
    135 Nc53283300dbf457ba9044da5401d952c rdf:first sg:person.01223441713.02
    136 rdf:rest Nb011d02c8afb4aa2938633029ba012e3
    137 Nc620ff7a5544418da43e6abc47469c57 schema:issueNumber 5
    138 rdf:type schema:PublicationIssue
    139 Nd4dee59428ce445682537f6309b18995 rdf:first sg:person.0774300251.64
    140 rdf:rest N7d9ed559beca4dfa89cb6c4c6a1063b2
    141 Ndda0a6b098ea45feb49a4ecf2d2278e4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    142 schema:name Proto-Oncogene Proteins c-myc
    143 rdf:type schema:DefinedTerm
    144 Ne6a1245f092e45af8a65dda4c558d3e9 schema:volumeNumber 28
    145 rdf:type schema:PublicationVolume
    146 Nea6cf4f52f9a4db1bf4810d3c75dd25a schema:name doi
    147 schema:value 10.1038/nbt.1621
    148 rdf:type schema:PropertyValue
    149 Nfb545a9845d247339a23ebf9e6788a66 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    150 schema:name Protein Isoforms
    151 rdf:type schema:DefinedTerm
    152 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    153 schema:name Biological Sciences
    154 rdf:type schema:DefinedTerm
    155 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    156 schema:name Genetics
    157 rdf:type schema:DefinedTerm
    158 sg:grant.2519905 http://pending.schema.org/fundedItem sg:pub.10.1038/nbt.1621
    159 rdf:type schema:MonetaryGrant
    160 sg:grant.2529425 http://pending.schema.org/fundedItem sg:pub.10.1038/nbt.1621
    161 rdf:type schema:MonetaryGrant
    162 sg:grant.2545461 http://pending.schema.org/fundedItem sg:pub.10.1038/nbt.1621
    163 rdf:type schema:MonetaryGrant
    164 sg:grant.2699343 http://pending.schema.org/fundedItem sg:pub.10.1038/nbt.1621
    165 rdf:type schema:MonetaryGrant
    166 sg:journal.1115214 schema:issn 1087-0156
    167 1546-1696
    168 schema:name Nature Biotechnology
    169 schema:publisher Springer Nature
    170 rdf:type schema:Periodical
    171 sg:person.01024612415.46 schema:affiliation grid-institutes:grid.164295.d
    172 schema:familyName Pertea
    173 schema:givenName Geo
    174 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024612415.46
    175 rdf:type schema:Person
    176 sg:person.01026162263.73 schema:affiliation grid-institutes:grid.20861.3d
    177 schema:familyName Wold
    178 schema:givenName Barbara J
    179 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01026162263.73
    180 rdf:type schema:Person
    181 sg:person.01042023041.45 schema:affiliation grid-institutes:grid.4367.6
    182 schema:familyName van Baren
    183 schema:givenName Marijke J
    184 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042023041.45
    185 rdf:type schema:Person
    186 sg:person.01223441713.02 schema:affiliation grid-institutes:grid.164295.d
    187 schema:familyName Salzberg
    188 schema:givenName Steven L
    189 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223441713.02
    190 rdf:type schema:Person
    191 sg:person.01247375013.30 schema:affiliation grid-institutes:grid.47840.3f
    192 schema:familyName Trapnell
    193 schema:givenName Cole
    194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247375013.30
    195 rdf:type schema:Person
    196 sg:person.0672165566.75 schema:affiliation grid-institutes:grid.47840.3f
    197 schema:familyName Pachter
    198 schema:givenName Lior
    199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0672165566.75
    200 rdf:type schema:Person
    201 sg:person.0673025131.06 schema:affiliation grid-institutes:grid.20861.3d
    202 schema:familyName Mortazavi
    203 schema:givenName Ali
    204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0673025131.06
    205 rdf:type schema:Person
    206 sg:person.0741140331.06 schema:affiliation grid-institutes:grid.20861.3d
    207 schema:familyName Williams
    208 schema:givenName Brian A
    209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741140331.06
    210 rdf:type schema:Person
    211 sg:person.0774300251.64 schema:affiliation grid-institutes:grid.20861.3d
    212 schema:familyName Kwan
    213 schema:givenName Gordon
    214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774300251.64
    215 rdf:type schema:Person
    216 sg:pub.10.1038/nature05676 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030633547
    217 https://doi.org/10.1038/nature05676
    218 rdf:type schema:CreativeWork
    219 sg:pub.10.1038/nature07509 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029002744
    220 https://doi.org/10.1038/nature07509
    221 rdf:type schema:CreativeWork
    222 sg:pub.10.1038/nature07638 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009442631
    223 https://doi.org/10.1038/nature07638
    224 rdf:type schema:CreativeWork
    225 sg:pub.10.1038/nature07672 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051133532
    226 https://doi.org/10.1038/nature07672
    227 rdf:type schema:CreativeWork
    228 sg:pub.10.1038/nature08195 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007963177
    229 https://doi.org/10.1038/nature08195
    230 rdf:type schema:CreativeWork
    231 sg:pub.10.1038/nmeth.1223 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048586936
    232 https://doi.org/10.1038/nmeth.1223
    233 rdf:type schema:CreativeWork
    234 sg:pub.10.1038/nmeth.1226 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045381177
    235 https://doi.org/10.1038/nmeth.1226
    236 rdf:type schema:CreativeWork
    237 sg:pub.10.1038/nmeth.1371 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011651858
    238 https://doi.org/10.1038/nmeth.1371
    239 rdf:type schema:CreativeWork
    240 sg:pub.10.1186/1471-2105-11-94 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053091615
    241 https://doi.org/10.1186/1471-2105-11-94
    242 rdf:type schema:CreativeWork
    243 sg:pub.10.1186/gb-2008-9-12-r175 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016469219
    244 https://doi.org/10.1186/gb-2008-9-12-r175
    245 rdf:type schema:CreativeWork
    246 sg:pub.10.1186/gb-2009-10-3-r25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049583368
    247 https://doi.org/10.1186/gb-2009-10-3-r25
    248 rdf:type schema:CreativeWork
    249 grid-institutes:grid.164295.d schema:alternateName Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    250 schema:name Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    251 Department of Computer Science, University of Maryland, College Park, Maryland, USA
    252 rdf:type schema:Organization
    253 grid-institutes:grid.20861.3d schema:alternateName Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA
    254 schema:name Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA
    255 rdf:type schema:Organization
    256 grid-institutes:grid.4367.6 schema:alternateName Genome Sciences Center, Washington University in St. Louis, St. Louis, Missouri, USA
    257 schema:name Genome Sciences Center, Washington University in St. Louis, St. Louis, Missouri, USA
    258 rdf:type schema:Organization
    259 grid-institutes:grid.47840.3f schema:alternateName Department of Computer Science, University of California, Berkeley, California, USA
    260 Department of Mathematics, University of California, Berkeley, California, USA
    261 schema:name Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    262 Department of Computer Science, University of California, Berkeley, California, USA
    263 Department of Computer Science, University of Maryland, College Park, Maryland, USA
    264 Department of Mathematics, University of California, Berkeley, California, USA
    265 Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
    266 rdf:type schema:Organization
     




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


    ...