Using TRIP for genome-wide position effect analysis in cultured cells View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2014-06

AUTHORS

Waseem Akhtar, Alexey V Pindyurin, Johann de Jong, Ludo Pagie, Jelle ten Hoeve, Anton Berns, Lodewyk F A Wessels, Bas van Steensel, Maarten van Lohuizen

ABSTRACT

The influence of local chromatin context on gene expression can be explored by integrating a transcription reporter at different locations in the genome as a sensor. Here we provide a detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level. TRIP is based on tagging each reporter with a unique barcode, which is used for independent reporter expression analysis and integration site mapping. Compared with previous methods for studying position effects, TRIP offers a 100-1,000-fold higher throughput in a faster and less-labor-intensive manner. The entire experimental protocol takes ∼42 d to complete, with high-throughput sequencing and data analysis requiring an additional ∼11 d. TRIP was developed by using transcription reporters in mouse embryonic stem (mES) cells, but because of its flexibility the method can be used to probe the influence of chromatin context on a variety of molecular processes in any transfectable cell line. More... »

PAGES

1255-1281

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nprot.2014.072

DOI

http://dx.doi.org/10.1038/nprot.2014.072

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1026024858

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24810036


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cells, Cultured", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromatin", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosomal Position Effects", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Transposable Elements", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Reporter", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genetic Vectors", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polynucleotides", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Antoni van Leeuwenhoek Hospital", 
          "id": "https://www.grid.ac/institutes/grid.430814.a", 
          "name": [
            "Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Akhtar", 
        "givenName": "Waseem", 
        "id": "sg:person.013752542234.80", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013752542234.80"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute of Molecular and Cell Biology", 
          "id": "https://www.grid.ac/institutes/grid.465302.6", 
          "name": [
            "Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.", 
            "Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pindyurin", 
        "givenName": "Alexey V", 
        "id": "sg:person.01354113157.90", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01354113157.90"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Antoni van Leeuwenhoek Hospital", 
          "id": "https://www.grid.ac/institutes/grid.430814.a", 
          "name": [
            "Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "de Jong", 
        "givenName": "Johann", 
        "id": "sg:person.0612722616.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0612722616.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Antoni van Leeuwenhoek Hospital", 
          "id": "https://www.grid.ac/institutes/grid.430814.a", 
          "name": [
            "Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pagie", 
        "givenName": "Ludo", 
        "id": "sg:person.01170342635.58", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01170342635.58"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Antoni van Leeuwenhoek Hospital", 
          "id": "https://www.grid.ac/institutes/grid.430814.a", 
          "name": [
            "Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hoeve", 
        "givenName": "Jelle ten", 
        "id": "sg:person.010600432677.17", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010600432677.17"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Skolkovo Institute of Science and Technology", 
          "id": "https://www.grid.ac/institutes/grid.454320.4", 
          "name": [
            "Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.", 
            "Skoltech Center for Stem Cell Research, Skolkovo Institute for Science and Technology, Skolkovo, Russia."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Berns", 
        "givenName": "Anton", 
        "id": "sg:person.015726612144.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015726612144.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Delft University of Technology", 
          "id": "https://www.grid.ac/institutes/grid.5292.c", 
          "name": [
            "Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.", 
            "Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wessels", 
        "givenName": "Lodewyk F A", 
        "id": "sg:person.013377553177.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013377553177.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Antoni van Leeuwenhoek Hospital", 
          "id": "https://www.grid.ac/institutes/grid.430814.a", 
          "name": [
            "Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "van Steensel", 
        "givenName": "Bas", 
        "id": "sg:person.01176344257.88", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01176344257.88"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Cancer Genomics Centre", 
          "id": "https://www.grid.ac/institutes/grid.450231.1", 
          "name": [
            "Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.", 
            "Cancer Genomics Centre, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "van Lohuizen", 
        "givenName": "Maarten", 
        "id": "sg:person.01000213306.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01000213306.89"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1038/mt.2012.126", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001010038"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/18.7.1687", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004205431"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1923", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006541515", 
          "https://doi.org/10.1038/nmeth.1923"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0065-2660(07)00001-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006596742"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1182/blood-2009-06-229757", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007088593"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gni043", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007486139"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1472-6750-11-28", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007691223", 
          "https://doi.org/10.1186/1472-6750-11-28"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.plasmid.2005.11.005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009846424"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks317", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011779291"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.6276007", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015510707"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2013.07.018", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019223722"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks309", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024334254"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pcbi.1001008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028198684"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-11-318", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031269250", 
          "https://doi.org/10.1186/1471-2164-11-318"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2007-8-s1-s8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032223789", 
          "https://doi.org/10.1186/gb-2007-8-s1-s8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1084/jem.20091175", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033102823"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2205", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033405287", 
          "https://doi.org/10.1038/nbt.2205"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s000180050262", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033658747", 
          "https://doi.org/10.1007/s000180050262"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nprot.2007.427", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035051131", 
          "https://doi.org/10.1038/nprot.2007.427"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0092-8674(84)90048-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035562084"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/23.9.1644", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038635285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg2008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038906443", 
          "https://doi.org/10.1038/nrg2008"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg2008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038906443", 
          "https://doi.org/10.1038/nrg2008"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.celrep.2012.12.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040298373"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm446", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045124061"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/emboj.2009.197", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045402745"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/emboj.2009.197", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045402745"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.790", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050216335", 
          "https://doi.org/10.1038/ng.790"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.9.14.1797", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050453984"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.090530797", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051271633"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/mt.2010.141", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053533109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.2448875", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062538000"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1079425218", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.239.4839.487", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1101677454"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2014-06", 
    "datePublishedReg": "2014-06-01", 
    "description": "The influence of local chromatin context on gene expression can be explored by integrating a transcription reporter at different locations in the genome as a sensor. Here we provide a detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level. TRIP is based on tagging each reporter with a unique barcode, which is used for independent reporter expression analysis and integration site mapping. Compared with previous methods for studying position effects, TRIP offers a 100-1,000-fold higher throughput in a faster and less-labor-intensive manner. The entire experimental protocol takes \u223c42 d to complete, with high-throughput sequencing and data analysis requiring an additional \u223c11 d. TRIP was developed by using transcription reporters in mouse embryonic stem (mES) cells, but because of its flexibility the method can be used to probe the influence of chromatin context on a variety of molecular processes in any transfectable cell line. ", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nprot.2014.072", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3789485", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1037502", 
        "issn": [
          "1754-2189", 
          "1750-2799"
        ], 
        "name": "Nature Protocols", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "Using TRIP for genome-wide position effect analysis in cultured cells", 
    "pagination": "1255-1281", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "7bfb0f01d204653e7272687381d6de06961f68b0c2c12e869c336105d96e8b26"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "24810036"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101284307"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nprot.2014.072"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1026024858"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nprot.2014.072", 
      "https://app.dimensions.ai/details/publication/pub.1026024858"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T22:37", 
    "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_8690_00000537.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/nprot/journal/v9/n6/full/nprot.2014.072.html"
  }
]
 

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/nprot.2014.072'

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/nprot.2014.072'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nprot.2014.072'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nprot.2014.072'


 

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

289 TRIPLES      21 PREDICATES      71 URIs      31 LITERALS      19 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nprot.2014.072 schema:about N0fa347dd527c44268777c8540bbc9a2b
2 N0fffc402aa554f59939f7f1460889b6f
3 N1cec866642bc42e38058bc1a0b28e338
4 N5ba89d3d1f3f41acaf823e49b134202b
5 N8942d8dabdf544e6b78e6962db77ca59
6 Na44b4ff01b064a839db042483bb48cab
7 Nb0025be2d9e34da4858da6cb439f89d0
8 Nbdc6dfdc7a8a4d6db80f443837fd1e9b
9 Nda1db8019bed4a7c96a82724d2fc5287
10 Nf8af806a0f3f4774ba8a8d9a4f74a216
11 anzsrc-for:06
12 anzsrc-for:0604
13 schema:author N81361455b75845dea2a974c2f9e8556e
14 schema:citation sg:pub.10.1007/s000180050262
15 sg:pub.10.1038/nbt.2205
16 sg:pub.10.1038/ng.790
17 sg:pub.10.1038/nmeth.1923
18 sg:pub.10.1038/nprot.2007.427
19 sg:pub.10.1038/nrg2008
20 sg:pub.10.1186/1471-2164-11-318
21 sg:pub.10.1186/1472-6750-11-28
22 sg:pub.10.1186/gb-2007-8-s1-s8
23 https://app.dimensions.ai/details/publication/pub.1079425218
24 https://doi.org/10.1016/0092-8674(84)90048-5
25 https://doi.org/10.1016/j.cell.2013.07.018
26 https://doi.org/10.1016/j.celrep.2012.12.003
27 https://doi.org/10.1016/j.plasmid.2005.11.005
28 https://doi.org/10.1016/s0065-2660(07)00001-6
29 https://doi.org/10.1038/emboj.2009.197
30 https://doi.org/10.1038/mt.2010.141
31 https://doi.org/10.1038/mt.2012.126
32 https://doi.org/10.1073/pnas.090530797
33 https://doi.org/10.1084/jem.20091175
34 https://doi.org/10.1093/nar/18.7.1687
35 https://doi.org/10.1093/nar/23.9.1644
36 https://doi.org/10.1093/nar/gkm446
37 https://doi.org/10.1093/nar/gks309
38 https://doi.org/10.1093/nar/gks317
39 https://doi.org/10.1093/nar/gni043
40 https://doi.org/10.1101/gad.9.14.1797
41 https://doi.org/10.1101/gr.6276007
42 https://doi.org/10.1126/science.239.4839.487
43 https://doi.org/10.1126/science.2448875
44 https://doi.org/10.1182/blood-2009-06-229757
45 https://doi.org/10.1371/journal.pcbi.1001008
46 schema:datePublished 2014-06
47 schema:datePublishedReg 2014-06-01
48 schema:description The influence of local chromatin context on gene expression can be explored by integrating a transcription reporter at different locations in the genome as a sensor. Here we provide a detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level. TRIP is based on tagging each reporter with a unique barcode, which is used for independent reporter expression analysis and integration site mapping. Compared with previous methods for studying position effects, TRIP offers a 100-1,000-fold higher throughput in a faster and less-labor-intensive manner. The entire experimental protocol takes ∼42 d to complete, with high-throughput sequencing and data analysis requiring an additional ∼11 d. TRIP was developed by using transcription reporters in mouse embryonic stem (mES) cells, but because of its flexibility the method can be used to probe the influence of chromatin context on a variety of molecular processes in any transfectable cell line.
49 schema:genre research_article
50 schema:inLanguage en
51 schema:isAccessibleForFree false
52 schema:isPartOf Nb998e87a50264adea7f38d59e9adaa85
53 Nc776a36af48d4517a060c10c58844a1c
54 sg:journal.1037502
55 schema:name Using TRIP for genome-wide position effect analysis in cultured cells
56 schema:pagination 1255-1281
57 schema:productId N2b1b6c35bdb54c958d0a81f85e0e9c95
58 N358661252be04d9898cedd89ef4eb976
59 N8c0b1932247a425fa4d6fe367c4da270
60 Nc4813134ac224799a01b7f7fe50648be
61 Nced1ff03b3334fac8d861e23aedfe0fe
62 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026024858
63 https://doi.org/10.1038/nprot.2014.072
64 schema:sdDatePublished 2019-04-10T22:37
65 schema:sdLicense https://scigraph.springernature.com/explorer/license/
66 schema:sdPublisher Nedc3870e001845e99ffe6612411ecd3b
67 schema:url http://www.nature.com/nprot/journal/v9/n6/full/nprot.2014.072.html
68 sgo:license sg:explorer/license/
69 sgo:sdDataset articles
70 rdf:type schema:ScholarlyArticle
71 N0fa347dd527c44268777c8540bbc9a2b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
72 schema:name High-Throughput Nucleotide Sequencing
73 rdf:type schema:DefinedTerm
74 N0fffc402aa554f59939f7f1460889b6f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
75 schema:name Cells, Cultured
76 rdf:type schema:DefinedTerm
77 N1cec866642bc42e38058bc1a0b28e338 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Genes, Reporter
79 rdf:type schema:DefinedTerm
80 N2b1b6c35bdb54c958d0a81f85e0e9c95 schema:name readcube_id
81 schema:value 7bfb0f01d204653e7272687381d6de06961f68b0c2c12e869c336105d96e8b26
82 rdf:type schema:PropertyValue
83 N2e04d2aa592e44789ff3524fd0df1d8e rdf:first sg:person.01170342635.58
84 rdf:rest N369ac9b285ee414a815fb3281eb59d67
85 N358661252be04d9898cedd89ef4eb976 schema:name nlm_unique_id
86 schema:value 101284307
87 rdf:type schema:PropertyValue
88 N369ac9b285ee414a815fb3281eb59d67 rdf:first sg:person.010600432677.17
89 rdf:rest N41ba3f2e87bb431c9b28a0c106f39204
90 N405abeb20bca493e9e3b750099860e53 rdf:first sg:person.01000213306.89
91 rdf:rest rdf:nil
92 N4165b89c711e4085b9d675b39be641eb rdf:first sg:person.01354113157.90
93 rdf:rest N9026ed6dc800498bbf401e0727467f53
94 N41ba3f2e87bb431c9b28a0c106f39204 rdf:first sg:person.015726612144.33
95 rdf:rest Nfc751bcf1a8a4d0abef68786b749c987
96 N5ba89d3d1f3f41acaf823e49b134202b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name DNA Transposable Elements
98 rdf:type schema:DefinedTerm
99 N81361455b75845dea2a974c2f9e8556e rdf:first sg:person.013752542234.80
100 rdf:rest N4165b89c711e4085b9d675b39be641eb
101 N8942d8dabdf544e6b78e6962db77ca59 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Genetic Vectors
103 rdf:type schema:DefinedTerm
104 N8a43af84b1e144cc8dbbdaa200484e83 rdf:first sg:person.01176344257.88
105 rdf:rest N405abeb20bca493e9e3b750099860e53
106 N8c0b1932247a425fa4d6fe367c4da270 schema:name dimensions_id
107 schema:value pub.1026024858
108 rdf:type schema:PropertyValue
109 N9026ed6dc800498bbf401e0727467f53 rdf:first sg:person.0612722616.08
110 rdf:rest N2e04d2aa592e44789ff3524fd0df1d8e
111 Na44b4ff01b064a839db042483bb48cab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name Chromosomal Position Effects
113 rdf:type schema:DefinedTerm
114 Nb0025be2d9e34da4858da6cb439f89d0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Chromatin
116 rdf:type schema:DefinedTerm
117 Nb998e87a50264adea7f38d59e9adaa85 schema:volumeNumber 9
118 rdf:type schema:PublicationVolume
119 Nbdc6dfdc7a8a4d6db80f443837fd1e9b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Mice
121 rdf:type schema:DefinedTerm
122 Nc4813134ac224799a01b7f7fe50648be schema:name doi
123 schema:value 10.1038/nprot.2014.072
124 rdf:type schema:PropertyValue
125 Nc776a36af48d4517a060c10c58844a1c schema:issueNumber 6
126 rdf:type schema:PublicationIssue
127 Nced1ff03b3334fac8d861e23aedfe0fe schema:name pubmed_id
128 schema:value 24810036
129 rdf:type schema:PropertyValue
130 Nda1db8019bed4a7c96a82724d2fc5287 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
131 schema:name Animals
132 rdf:type schema:DefinedTerm
133 Nedc3870e001845e99ffe6612411ecd3b schema:name Springer Nature - SN SciGraph project
134 rdf:type schema:Organization
135 Nf8af806a0f3f4774ba8a8d9a4f74a216 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Polynucleotides
137 rdf:type schema:DefinedTerm
138 Nfc751bcf1a8a4d0abef68786b749c987 rdf:first sg:person.013377553177.45
139 rdf:rest N8a43af84b1e144cc8dbbdaa200484e83
140 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
141 schema:name Biological Sciences
142 rdf:type schema:DefinedTerm
143 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
144 schema:name Genetics
145 rdf:type schema:DefinedTerm
146 sg:grant.3789485 http://pending.schema.org/fundedItem sg:pub.10.1038/nprot.2014.072
147 rdf:type schema:MonetaryGrant
148 sg:journal.1037502 schema:issn 1750-2799
149 1754-2189
150 schema:name Nature Protocols
151 rdf:type schema:Periodical
152 sg:person.01000213306.89 schema:affiliation https://www.grid.ac/institutes/grid.450231.1
153 schema:familyName van Lohuizen
154 schema:givenName Maarten
155 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01000213306.89
156 rdf:type schema:Person
157 sg:person.010600432677.17 schema:affiliation https://www.grid.ac/institutes/grid.430814.a
158 schema:familyName Hoeve
159 schema:givenName Jelle ten
160 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010600432677.17
161 rdf:type schema:Person
162 sg:person.01170342635.58 schema:affiliation https://www.grid.ac/institutes/grid.430814.a
163 schema:familyName Pagie
164 schema:givenName Ludo
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01170342635.58
166 rdf:type schema:Person
167 sg:person.01176344257.88 schema:affiliation https://www.grid.ac/institutes/grid.430814.a
168 schema:familyName van Steensel
169 schema:givenName Bas
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01176344257.88
171 rdf:type schema:Person
172 sg:person.013377553177.45 schema:affiliation https://www.grid.ac/institutes/grid.5292.c
173 schema:familyName Wessels
174 schema:givenName Lodewyk F A
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013377553177.45
176 rdf:type schema:Person
177 sg:person.01354113157.90 schema:affiliation https://www.grid.ac/institutes/grid.465302.6
178 schema:familyName Pindyurin
179 schema:givenName Alexey V
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01354113157.90
181 rdf:type schema:Person
182 sg:person.013752542234.80 schema:affiliation https://www.grid.ac/institutes/grid.430814.a
183 schema:familyName Akhtar
184 schema:givenName Waseem
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013752542234.80
186 rdf:type schema:Person
187 sg:person.015726612144.33 schema:affiliation https://www.grid.ac/institutes/grid.454320.4
188 schema:familyName Berns
189 schema:givenName Anton
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015726612144.33
191 rdf:type schema:Person
192 sg:person.0612722616.08 schema:affiliation https://www.grid.ac/institutes/grid.430814.a
193 schema:familyName de Jong
194 schema:givenName Johann
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0612722616.08
196 rdf:type schema:Person
197 sg:pub.10.1007/s000180050262 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033658747
198 https://doi.org/10.1007/s000180050262
199 rdf:type schema:CreativeWork
200 sg:pub.10.1038/nbt.2205 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033405287
201 https://doi.org/10.1038/nbt.2205
202 rdf:type schema:CreativeWork
203 sg:pub.10.1038/ng.790 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050216335
204 https://doi.org/10.1038/ng.790
205 rdf:type schema:CreativeWork
206 sg:pub.10.1038/nmeth.1923 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006541515
207 https://doi.org/10.1038/nmeth.1923
208 rdf:type schema:CreativeWork
209 sg:pub.10.1038/nprot.2007.427 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035051131
210 https://doi.org/10.1038/nprot.2007.427
211 rdf:type schema:CreativeWork
212 sg:pub.10.1038/nrg2008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038906443
213 https://doi.org/10.1038/nrg2008
214 rdf:type schema:CreativeWork
215 sg:pub.10.1186/1471-2164-11-318 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031269250
216 https://doi.org/10.1186/1471-2164-11-318
217 rdf:type schema:CreativeWork
218 sg:pub.10.1186/1472-6750-11-28 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007691223
219 https://doi.org/10.1186/1472-6750-11-28
220 rdf:type schema:CreativeWork
221 sg:pub.10.1186/gb-2007-8-s1-s8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032223789
222 https://doi.org/10.1186/gb-2007-8-s1-s8
223 rdf:type schema:CreativeWork
224 https://app.dimensions.ai/details/publication/pub.1079425218 schema:CreativeWork
225 https://doi.org/10.1016/0092-8674(84)90048-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035562084
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1016/j.cell.2013.07.018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019223722
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1016/j.celrep.2012.12.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040298373
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1016/j.plasmid.2005.11.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009846424
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1016/s0065-2660(07)00001-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006596742
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1038/emboj.2009.197 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045402745
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1038/mt.2010.141 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053533109
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1038/mt.2012.126 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001010038
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1073/pnas.090530797 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051271633
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1084/jem.20091175 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033102823
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1093/nar/18.7.1687 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004205431
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1093/nar/23.9.1644 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038635285
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1093/nar/gkm446 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045124061
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1093/nar/gks309 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024334254
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1093/nar/gks317 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011779291
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1093/nar/gni043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007486139
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1101/gad.9.14.1797 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050453984
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1101/gr.6276007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015510707
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1126/science.239.4839.487 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101677454
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1126/science.2448875 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062538000
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1182/blood-2009-06-229757 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007088593
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1371/journal.pcbi.1001008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028198684
268 rdf:type schema:CreativeWork
269 https://www.grid.ac/institutes/grid.430814.a schema:alternateName Antoni van Leeuwenhoek Hospital
270 schema:name Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
271 Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
272 Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
273 rdf:type schema:Organization
274 https://www.grid.ac/institutes/grid.450231.1 schema:alternateName Cancer Genomics Centre
275 schema:name Cancer Genomics Centre, The Netherlands.
276 Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
277 rdf:type schema:Organization
278 https://www.grid.ac/institutes/grid.454320.4 schema:alternateName Skolkovo Institute of Science and Technology
279 schema:name Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
280 Skoltech Center for Stem Cell Research, Skolkovo Institute for Science and Technology, Skolkovo, Russia.
281 rdf:type schema:Organization
282 https://www.grid.ac/institutes/grid.465302.6 schema:alternateName Institute of Molecular and Cell Biology
283 schema:name Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
284 Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.
285 rdf:type schema:Organization
286 https://www.grid.ac/institutes/grid.5292.c schema:alternateName Delft University of Technology
287 schema:name Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
288 Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
289 rdf:type schema:Organization
 




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


...