Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2003-10

AUTHORS

John Castle, Phil Garrett-Engele, Christopher D Armour, Sven J Duenwald, Patrick M Loerch, Michael R Meyer, Eric E Schadt, Roland Stoughton, Mark L Parrish, Daniel D Shoemaker, Jason M Johnson

ABSTRACT

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing. More... »

PAGES

r66

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/gb-2003-4-10-r66

DOI

http://dx.doi.org/10.1186/gb-2003-4-10-r66

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1024685309

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/14519201


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": "Alternative Splicing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Annexin A7", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Exons", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Introns", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "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": "RNA Splice Sites", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Messenger", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Retinoblastoma", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reverse Transcriptase Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Castle", 
        "givenName": "John", 
        "id": "sg:person.0631450510.27", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0631450510.27"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Garrett-Engele", 
        "givenName": "Phil", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Armour", 
        "givenName": "Christopher D", 
        "id": "sg:person.01362511052.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01362511052.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Duenwald", 
        "givenName": "Sven J", 
        "id": "sg:person.01336063544.09", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01336063544.09"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Loerch", 
        "givenName": "Patrick M", 
        "id": "sg:person.01024140760.37", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024140760.37"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Meyer", 
        "givenName": "Michael R", 
        "id": "sg:person.01022474742.72", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022474742.72"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schadt", 
        "givenName": "Eric E", 
        "id": "sg:person.0774556547.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774556547.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stoughton", 
        "givenName": "Roland", 
        "id": "sg:person.0655372240.53", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655372240.53"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Parrish", 
        "givenName": "Mark L", 
        "id": "sg:person.0643503042.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0643503042.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shoemaker", 
        "givenName": "Daniel D", 
        "id": "sg:person.0607257040.49", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0607257040.49"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Johnson", 
        "givenName": "Jason M", 
        "id": "sg:person.01132625164.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01132625164.05"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1101/gr.155001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001220379"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt0402-353", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005630083", 
          "https://doi.org/10.1038/nbt0402-353"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt0402-353", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005630083", 
          "https://doi.org/10.1038/nbt0402-353"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/74153", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006163608", 
          "https://doi.org/10.1038/74153"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/74153", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006163608", 
          "https://doi.org/10.1038/74153"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/86730", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013279521", 
          "https://doi.org/10.1038/86730"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/86730", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013279521", 
          "https://doi.org/10.1038/86730"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/29.13.2850", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014048616"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0014-5793(00)01581-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014937581"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btg1044", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017020972"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.9.12.1288", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018310168"
        ], 
        "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": "https://doi.org/10.1016/s0968-0004(00)01549-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031925448"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/323643a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033717519", 
          "https://doi.org/10.1038/323643a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/418236a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039558582", 
          "https://doi.org/10.1038/418236a"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/418236a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039558582", 
          "https://doi.org/10.1038/418236a"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/418236a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039558582", 
          "https://doi.org/10.1038/418236a"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.220302", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040844943"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkf492", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041173262"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.191702", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042036090"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/85772", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042673420", 
          "https://doi.org/10.1038/85772"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/85772", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042673420", 
          "https://doi.org/10.1038/85772"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057062", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042854081", 
          "https://doi.org/10.1038/35057062"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057062", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042854081", 
          "https://doi.org/10.1038/35057062"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/27.13.2627", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048678717"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(00)00128-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049614900"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.165501", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051259029"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057141", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053314410", 
          "https://doi.org/10.1038/35057141"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057141", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053314410", 
          "https://doi.org/10.1038/35057141"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/28.21.4364", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053716700"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1086/514856", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058789342"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1068597", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062445839"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1069415", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062445909"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.287.5454.873", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062568256"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.188001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1074949074"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1077603651", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.8.9.967", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1083321060"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2003-10", 
    "datePublishedReg": "2003-10-01", 
    "description": "Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/gb-2003-4-10-r66", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023439", 
        "issn": [
          "1474-760X", 
          "1465-6906"
        ], 
        "name": "Genome Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "10", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "4"
      }
    ], 
    "name": "Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing", 
    "pagination": "r66", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "7599e74d5c9dbd420ad6a8a5cef0f299e0c6cbc170977c4e9c229d1271673ff9"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "14519201"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100960660"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/gb-2003-4-10-r66"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1024685309"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/gb-2003-4-10-r66", 
      "https://app.dimensions.ai/details/publication/pub.1024685309"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T16:42", 
    "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_8669_00000512.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2Fgb-2003-4-10-r66"
  }
]
 

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/gb-2003-4-10-r66'

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/gb-2003-4-10-r66'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gb-2003-4-10-r66'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gb-2003-4-10-r66'


 

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

300 TRIPLES      21 PREDICATES      70 URIs      33 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/gb-2003-4-10-r66 schema:about N02a069a1e6bc4a579f3a5b2dd3fba15f
2 N11fb573fa65f4c0b9808d5db2c74f4e6
3 N16f6720dd95f4ddb8bb51a777179b01b
4 N2bad54263a354376b38167ecffd1d96a
5 N3c4d5bfc1ea2418f9e7c435133c75b74
6 N3f39c4c673ad455abcd1cc2760679127
7 N78ec8ae7c7c44044a69756a1e4c5ce77
8 N7e0451bdfd244d3c87714b7ccde4954a
9 N8441ed0bc05940b4a45bbf210238978b
10 N9ab6b23bb268476fb2cc3b4cd4127af8
11 Nbea75477771d49f8a45342df500609c0
12 Nf1a6b7ac4c1e415788c4d477c67e7ce7
13 anzsrc-for:06
14 anzsrc-for:0604
15 schema:author N9d114087bcc94ac2972c5d527e8bb7a9
16 schema:citation sg:pub.10.1038/323643a0
17 sg:pub.10.1038/35057062
18 sg:pub.10.1038/35057141
19 sg:pub.10.1038/418236a
20 sg:pub.10.1038/74153
21 sg:pub.10.1038/85772
22 sg:pub.10.1038/86730
23 sg:pub.10.1038/nbt0402-353
24 sg:pub.10.1038/ng0102-13
25 https://app.dimensions.ai/details/publication/pub.1077603651
26 https://doi.org/10.1016/s0014-5793(00)01581-7
27 https://doi.org/10.1016/s0092-8674(00)00128-8
28 https://doi.org/10.1016/s0968-0004(00)01549-8
29 https://doi.org/10.1086/514856
30 https://doi.org/10.1093/bioinformatics/btg1044
31 https://doi.org/10.1093/nar/27.13.2627
32 https://doi.org/10.1093/nar/28.21.4364
33 https://doi.org/10.1093/nar/29.13.2850
34 https://doi.org/10.1093/nar/gkf492
35 https://doi.org/10.1101/gr.155001
36 https://doi.org/10.1101/gr.165501
37 https://doi.org/10.1101/gr.188001
38 https://doi.org/10.1101/gr.191702
39 https://doi.org/10.1101/gr.220302
40 https://doi.org/10.1101/gr.8.9.967
41 https://doi.org/10.1101/gr.9.12.1288
42 https://doi.org/10.1126/science.1068597
43 https://doi.org/10.1126/science.1069415
44 https://doi.org/10.1126/science.287.5454.873
45 schema:datePublished 2003-10
46 schema:datePublishedReg 2003-10-01
47 schema:description Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.
48 schema:genre research_article
49 schema:inLanguage en
50 schema:isAccessibleForFree true
51 schema:isPartOf N4b4d5626166d4ab3b94d4b20f22f4ac7
52 Ne421c2b3054e45ffa316d40ddd2cf7b7
53 sg:journal.1023439
54 schema:name Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing
55 schema:pagination r66
56 schema:productId N3bb0774e295844149a909fb6677a1d52
57 N5e0f1c8de6b14ee495f4ac70eb377c49
58 Na2ca219142784a3ba850ae101a2ad069
59 Na3fab542dbea44028eff2e0359cf0785
60 Nd1a5670320f44ffa934151057d2b35a5
61 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024685309
62 https://doi.org/10.1186/gb-2003-4-10-r66
63 schema:sdDatePublished 2019-04-10T16:42
64 schema:sdLicense https://scigraph.springernature.com/explorer/license/
65 schema:sdPublisher N6ff4edc1d1c04166ae009cb6bff41da6
66 schema:url http://link.springer.com/10.1186%2Fgb-2003-4-10-r66
67 sgo:license sg:explorer/license/
68 sgo:sdDataset articles
69 rdf:type schema:ScholarlyArticle
70 N02a069a1e6bc4a579f3a5b2dd3fba15f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
71 schema:name RNA, Messenger
72 rdf:type schema:DefinedTerm
73 N0c75d8db5c3e4d199399fac8424040b2 schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
74 rdf:type schema:Organization
75 N11fb573fa65f4c0b9808d5db2c74f4e6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
76 schema:name Protein Isoforms
77 rdf:type schema:DefinedTerm
78 N16f6720dd95f4ddb8bb51a777179b01b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
79 schema:name Annexin A7
80 rdf:type schema:DefinedTerm
81 N2a82c5b7f9b449748f77b5fd206b3cc2 schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
82 rdf:type schema:Organization
83 N2aeb1ad0f61f4003b676d64f2c5262fe schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
84 rdf:type schema:Organization
85 N2bad54263a354376b38167ecffd1d96a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Introns
87 rdf:type schema:DefinedTerm
88 N3bb0774e295844149a909fb6677a1d52 schema:name doi
89 schema:value 10.1186/gb-2003-4-10-r66
90 rdf:type schema:PropertyValue
91 N3c4d5bfc1ea2418f9e7c435133c75b74 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Molecular Sequence Data
93 rdf:type schema:DefinedTerm
94 N3e81c3254e9046d89b0f9831e60a25db rdf:first sg:person.01336063544.09
95 rdf:rest N875b81cef33641a6a99f8f95fa0f54b8
96 N3f39c4c673ad455abcd1cc2760679127 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name Humans
98 rdf:type schema:DefinedTerm
99 N3f41ad7d077344fe8773a3ca09870c3e schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
100 rdf:type schema:Organization
101 N4b4d5626166d4ab3b94d4b20f22f4ac7 schema:issueNumber 10
102 rdf:type schema:PublicationIssue
103 N57a1b44bb7154adc8436fbb37c0f9a55 rdf:first sg:person.01132625164.05
104 rdf:rest rdf:nil
105 N598a7097cdba4420a47c1d6b527e42b4 rdf:first sg:person.0655372240.53
106 rdf:rest Ne050f83ace1b4084ae71b0a9323d16d1
107 N5e0f1c8de6b14ee495f4ac70eb377c49 schema:name readcube_id
108 schema:value 7599e74d5c9dbd420ad6a8a5cef0f299e0c6cbc170977c4e9c229d1271673ff9
109 rdf:type schema:PropertyValue
110 N5e92a09095794b0e8a488aed1c4a313c schema:affiliation N0c75d8db5c3e4d199399fac8424040b2
111 schema:familyName Garrett-Engele
112 schema:givenName Phil
113 rdf:type schema:Person
114 N6341d445ea594ac9b745bf7bad1a19a0 rdf:first N5e92a09095794b0e8a488aed1c4a313c
115 rdf:rest N6e4d476d0e3c489193f527ed92fe82e3
116 N6e4d476d0e3c489193f527ed92fe82e3 rdf:first sg:person.01362511052.02
117 rdf:rest N3e81c3254e9046d89b0f9831e60a25db
118 N6ff4edc1d1c04166ae009cb6bff41da6 schema:name Springer Nature - SN SciGraph project
119 rdf:type schema:Organization
120 N78ec8ae7c7c44044a69756a1e4c5ce77 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
121 schema:name RNA Splice Sites
122 rdf:type schema:DefinedTerm
123 N7e0451bdfd244d3c87714b7ccde4954a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Alternative Splicing
125 rdf:type schema:DefinedTerm
126 N8441ed0bc05940b4a45bbf210238978b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name Retinoblastoma
128 rdf:type schema:DefinedTerm
129 N875b81cef33641a6a99f8f95fa0f54b8 rdf:first sg:person.01024140760.37
130 rdf:rest Na6688c3048464e2cb873ae437e1c8e6d
131 N87e1271d213d4ad9bda8ed5f96743958 schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
132 rdf:type schema:Organization
133 N8b1e5da0507142fdb893252c3b3653cf schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
134 rdf:type schema:Organization
135 N9ab6b23bb268476fb2cc3b4cd4127af8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Oligonucleotide Array Sequence Analysis
137 rdf:type schema:DefinedTerm
138 N9d114087bcc94ac2972c5d527e8bb7a9 rdf:first sg:person.0631450510.27
139 rdf:rest N6341d445ea594ac9b745bf7bad1a19a0
140 Na2ca219142784a3ba850ae101a2ad069 schema:name dimensions_id
141 schema:value pub.1024685309
142 rdf:type schema:PropertyValue
143 Na3fab542dbea44028eff2e0359cf0785 schema:name nlm_unique_id
144 schema:value 100960660
145 rdf:type schema:PropertyValue
146 Na6688c3048464e2cb873ae437e1c8e6d rdf:first sg:person.01022474742.72
147 rdf:rest Nd5161afae2a841c385e69061497241a1
148 Na97ece677caa4320b3f5f148e6110f9e schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
149 rdf:type schema:Organization
150 Nbea75477771d49f8a45342df500609c0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
151 schema:name Exons
152 rdf:type schema:DefinedTerm
153 Nc094be306c004da0a74b6b76210dfced schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
154 rdf:type schema:Organization
155 Nd1a5670320f44ffa934151057d2b35a5 schema:name pubmed_id
156 schema:value 14519201
157 rdf:type schema:PropertyValue
158 Nd5161afae2a841c385e69061497241a1 rdf:first sg:person.0774556547.46
159 rdf:rest N598a7097cdba4420a47c1d6b527e42b4
160 Ndbaf9b0592b94781b8a6092805a2ce21 schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
161 rdf:type schema:Organization
162 Ne050f83ace1b4084ae71b0a9323d16d1 rdf:first sg:person.0643503042.33
163 rdf:rest Nefddd929210c445cbcf13e194e21a46a
164 Ne421c2b3054e45ffa316d40ddd2cf7b7 schema:volumeNumber 4
165 rdf:type schema:PublicationVolume
166 Nefddd929210c445cbcf13e194e21a46a rdf:first sg:person.0607257040.49
167 rdf:rest N57a1b44bb7154adc8436fbb37c0f9a55
168 Nf1a6b7ac4c1e415788c4d477c67e7ce7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
169 schema:name Reverse Transcriptase Polymerase Chain Reaction
170 rdf:type schema:DefinedTerm
171 Nf38fc5e57db04b2f971476fe2746fd9b schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
172 rdf:type schema:Organization
173 Nf4fc4cade9a94a91bcecfd77f999dfd3 schema:name Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, 98034, Kirkland, Washington, USA
174 rdf:type schema:Organization
175 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
176 schema:name Biological Sciences
177 rdf:type schema:DefinedTerm
178 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
179 schema:name Genetics
180 rdf:type schema:DefinedTerm
181 sg:journal.1023439 schema:issn 1465-6906
182 1474-760X
183 schema:name Genome Biology
184 rdf:type schema:Periodical
185 sg:person.01022474742.72 schema:affiliation Nf4fc4cade9a94a91bcecfd77f999dfd3
186 schema:familyName Meyer
187 schema:givenName Michael R
188 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022474742.72
189 rdf:type schema:Person
190 sg:person.01024140760.37 schema:affiliation N8b1e5da0507142fdb893252c3b3653cf
191 schema:familyName Loerch
192 schema:givenName Patrick M
193 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024140760.37
194 rdf:type schema:Person
195 sg:person.01132625164.05 schema:affiliation N2a82c5b7f9b449748f77b5fd206b3cc2
196 schema:familyName Johnson
197 schema:givenName Jason M
198 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01132625164.05
199 rdf:type schema:Person
200 sg:person.01336063544.09 schema:affiliation Nf38fc5e57db04b2f971476fe2746fd9b
201 schema:familyName Duenwald
202 schema:givenName Sven J
203 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01336063544.09
204 rdf:type schema:Person
205 sg:person.01362511052.02 schema:affiliation N2aeb1ad0f61f4003b676d64f2c5262fe
206 schema:familyName Armour
207 schema:givenName Christopher D
208 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01362511052.02
209 rdf:type schema:Person
210 sg:person.0607257040.49 schema:affiliation N3f41ad7d077344fe8773a3ca09870c3e
211 schema:familyName Shoemaker
212 schema:givenName Daniel D
213 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0607257040.49
214 rdf:type schema:Person
215 sg:person.0631450510.27 schema:affiliation Na97ece677caa4320b3f5f148e6110f9e
216 schema:familyName Castle
217 schema:givenName John
218 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0631450510.27
219 rdf:type schema:Person
220 sg:person.0643503042.33 schema:affiliation Nc094be306c004da0a74b6b76210dfced
221 schema:familyName Parrish
222 schema:givenName Mark L
223 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0643503042.33
224 rdf:type schema:Person
225 sg:person.0655372240.53 schema:affiliation Ndbaf9b0592b94781b8a6092805a2ce21
226 schema:familyName Stoughton
227 schema:givenName Roland
228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655372240.53
229 rdf:type schema:Person
230 sg:person.0774556547.46 schema:affiliation N87e1271d213d4ad9bda8ed5f96743958
231 schema:familyName Schadt
232 schema:givenName Eric E
233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774556547.46
234 rdf:type schema:Person
235 sg:pub.10.1038/323643a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033717519
236 https://doi.org/10.1038/323643a0
237 rdf:type schema:CreativeWork
238 sg:pub.10.1038/35057062 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042854081
239 https://doi.org/10.1038/35057062
240 rdf:type schema:CreativeWork
241 sg:pub.10.1038/35057141 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053314410
242 https://doi.org/10.1038/35057141
243 rdf:type schema:CreativeWork
244 sg:pub.10.1038/418236a schema:sameAs https://app.dimensions.ai/details/publication/pub.1039558582
245 https://doi.org/10.1038/418236a
246 rdf:type schema:CreativeWork
247 sg:pub.10.1038/74153 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006163608
248 https://doi.org/10.1038/74153
249 rdf:type schema:CreativeWork
250 sg:pub.10.1038/85772 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042673420
251 https://doi.org/10.1038/85772
252 rdf:type schema:CreativeWork
253 sg:pub.10.1038/86730 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013279521
254 https://doi.org/10.1038/86730
255 rdf:type schema:CreativeWork
256 sg:pub.10.1038/nbt0402-353 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005630083
257 https://doi.org/10.1038/nbt0402-353
258 rdf:type schema:CreativeWork
259 sg:pub.10.1038/ng0102-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025102244
260 https://doi.org/10.1038/ng0102-13
261 rdf:type schema:CreativeWork
262 https://app.dimensions.ai/details/publication/pub.1077603651 schema:CreativeWork
263 https://doi.org/10.1016/s0014-5793(00)01581-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014937581
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1016/s0092-8674(00)00128-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049614900
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1016/s0968-0004(00)01549-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031925448
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1086/514856 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058789342
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1093/bioinformatics/btg1044 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017020972
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1093/nar/27.13.2627 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048678717
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1093/nar/28.21.4364 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053716700
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1093/nar/29.13.2850 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014048616
278 rdf:type schema:CreativeWork
279 https://doi.org/10.1093/nar/gkf492 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041173262
280 rdf:type schema:CreativeWork
281 https://doi.org/10.1101/gr.155001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001220379
282 rdf:type schema:CreativeWork
283 https://doi.org/10.1101/gr.165501 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051259029
284 rdf:type schema:CreativeWork
285 https://doi.org/10.1101/gr.188001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1074949074
286 rdf:type schema:CreativeWork
287 https://doi.org/10.1101/gr.191702 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042036090
288 rdf:type schema:CreativeWork
289 https://doi.org/10.1101/gr.220302 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040844943
290 rdf:type schema:CreativeWork
291 https://doi.org/10.1101/gr.8.9.967 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083321060
292 rdf:type schema:CreativeWork
293 https://doi.org/10.1101/gr.9.12.1288 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018310168
294 rdf:type schema:CreativeWork
295 https://doi.org/10.1126/science.1068597 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062445839
296 rdf:type schema:CreativeWork
297 https://doi.org/10.1126/science.1069415 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062445909
298 rdf:type schema:CreativeWork
299 https://doi.org/10.1126/science.287.5454.873 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062568256
300 rdf:type schema:CreativeWork
 




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


...