Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-12

AUTHORS

John G Doench, Ella Hartenian, Daniel B Graham, Zuzana Tothova, Mudra Hegde, Ian Smith, Meagan Sullender, Benjamin L Ebert, Ramnik J Xavier, David E Root

ABSTRACT

Components of the prokaryotic clustered, regularly interspaced, short palindromic repeats (CRISPR) loci have recently been repurposed for use in mammalian cells. The CRISPR-associated (Cas)9 can be programmed with a single guide RNA (sgRNA) to generate site-specific DNA breaks, but there are few known rules governing on-target efficacy of this system. We created a pool of sgRNAs, tiling across all possible target sites of a panel of six endogenous mouse and three endogenous human genes and quantitatively assessed their ability to produce null alleles of their target gene by antibody staining and flow cytometry. We discovered sequence features that improved activity, including a further optimization of the protospacer-adjacent motif (PAM) of Streptococcus pyogenes Cas9. The results from 1,841 sgRNAs were used to construct a predictive model of sgRNA activity to improve sgRNA design for gene editing and genetic screens. We provide an online tool for the design of highly active sgRNAs for any gene of interest. More... »

PAGES

1262-1267

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt.3026

DOI

http://dx.doi.org/10.1038/nbt.3026

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1033528408

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25184501


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": "CRISPR-Cas Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Flow Cytometry", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Silencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Targeting", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Streptococcus pyogenes", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Doench", 
        "givenName": "John G", 
        "id": "sg:person.0603505234.56", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0603505234.56"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hartenian", 
        "givenName": "Ella", 
        "id": "sg:person.01333575730.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333575730.40"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Graham", 
        "givenName": "Daniel B", 
        "id": "sg:person.01123503121.96", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123503121.96"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.", 
            "Brigham and Women's Hospital, Harvard Medical School, Department of Medicine, Division of Hematology, Boston, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tothova", 
        "givenName": "Zuzana", 
        "id": "sg:person.01223156657.41", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223156657.41"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hegde", 
        "givenName": "Mudra", 
        "id": "sg:person.0753252352.23", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0753252352.23"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Smith", 
        "givenName": "Ian", 
        "id": "sg:person.01021365552.11", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021365552.11"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sullender", 
        "givenName": "Meagan", 
        "id": "sg:person.01067500752.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01067500752.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.", 
            "Brigham and Women's Hospital, Harvard Medical School, Department of Medicine, Division of Hematology, Boston, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ebert", 
        "givenName": "Benjamin L", 
        "id": "sg:person.01052352713.61", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01052352713.61"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Harvard University", 
          "id": "https://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.", 
            "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.", 
            "Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Xavier", 
        "givenName": "Ramnik J", 
        "id": "sg:person.0717130066.82", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Root", 
        "givenName": "David E", 
        "id": "sg:person.01270622506.69", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01270622506.69"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1126/science.1247005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007966801"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1247005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007966801"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2623", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009511624", 
          "https://doi.org/10.1038/nbt.2623"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09523", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009515358", 
          "https://doi.org/10.1038/nature09523"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09523", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009515358", 
          "https://doi.org/10.1038/nature09523"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.162339.113", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010306401"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1109363108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012211256"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2647", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012543463", 
          "https://doi.org/10.1038/nbt.2647"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1231143", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019873131"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2508", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019888616", 
          "https://doi.org/10.1038/nbt.2508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1232033", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022072971"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.7554/elife.00471", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023633935"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature13166", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027499136", 
          "https://doi.org/10.1038/nature13166"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0098186", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029929613"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2013.08.022", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034724285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1138140", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036312168"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0506580102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037705714"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0506580102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037705714"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt936", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039709400", 
          "https://doi.org/10.1038/nbt936"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt936", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039709400", 
          "https://doi.org/10.1038/nbt936"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2800", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041802825", 
          "https://doi.org/10.1038/nbt.2800"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1225829", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041850060"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2916", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043348902", 
          "https://doi.org/10.1038/nbt.2916"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2889", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043519930", 
          "https://doi.org/10.1038/nbt.2889"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1246981", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043810806"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1246981", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043810806"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2011.02.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043964993"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2808", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048637524", 
          "https://doi.org/10.1038/nbt.2808"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkr606", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052438070"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0810485105", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053380624"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2014-12", 
    "datePublishedReg": "2014-12-01", 
    "description": "Components of the prokaryotic clustered, regularly interspaced, short palindromic repeats (CRISPR) loci have recently been repurposed for use in mammalian cells. The CRISPR-associated (Cas)9 can be programmed with a single guide RNA (sgRNA) to generate site-specific DNA breaks, but there are few known rules governing on-target efficacy of this system. We created a pool of sgRNAs, tiling across all possible target sites of a panel of six endogenous mouse and three endogenous human genes and quantitatively assessed their ability to produce null alleles of their target gene by antibody staining and flow cytometry. We discovered sequence features that improved activity, including a further optimization of the protospacer-adjacent motif (PAM) of Streptococcus pyogenes Cas9. The results from 1,841 sgRNAs were used to construct a predictive model of sgRNA activity to improve sgRNA design for gene editing and genetic screens. We provide an online tool for the design of highly active sgRNAs for any gene of interest. ", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nbt.3026", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2682491", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2439002", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3493714", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1115214", 
        "issn": [
          "1087-0156", 
          "1546-1696"
        ], 
        "name": "Nature Biotechnology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "12", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "32"
      }
    ], 
    "name": "Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation", 
    "pagination": "1262-1267", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "9fb88c6042d089b73a95612380375076a25f49c042b160e63d94c95488362632"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "25184501"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "9604648"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nbt.3026"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1033528408"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nbt.3026", 
      "https://app.dimensions.ai/details/publication/pub.1033528408"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T18:08", 
    "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_8675_00000425.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/nbt/journal/v32/n12/full/nbt.3026.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/nbt.3026'

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.3026'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.3026'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt.3026'


 

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

265 TRIPLES      21 PREDICATES      63 URIs      30 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nbt.3026 schema:about N05479a66d889422cbdc6ffa6df88ee62
2 N0ad67a5aceee4a64b0848f297bcc4bfc
3 N26a31af1554142b194eca5da3ef11443
4 N4350860d3db54a5a83e5b438ff6e9807
5 N43aa1a7c2bdd49c09fb6c6f35d6d9528
6 N74ec2a9ee295476d8a2f6451cb89ccf7
7 N7b0dff89bf28441b9d660e822fc32a53
8 Nca40c7a4594e4657843ca9b9673c8ff3
9 Nf26102be0246456ca1541aefe3c38833
10 anzsrc-for:06
11 anzsrc-for:0604
12 schema:author N002b1582f3a4464bb318f10c7b906835
13 schema:citation sg:pub.10.1038/nature09523
14 sg:pub.10.1038/nature13166
15 sg:pub.10.1038/nbt.2508
16 sg:pub.10.1038/nbt.2623
17 sg:pub.10.1038/nbt.2647
18 sg:pub.10.1038/nbt.2800
19 sg:pub.10.1038/nbt.2808
20 sg:pub.10.1038/nbt.2889
21 sg:pub.10.1038/nbt.2916
22 sg:pub.10.1038/nbt936
23 https://doi.org/10.1016/j.cell.2013.08.022
24 https://doi.org/10.1016/j.molcel.2011.02.008
25 https://doi.org/10.1073/pnas.0506580102
26 https://doi.org/10.1073/pnas.0810485105
27 https://doi.org/10.1073/pnas.1109363108
28 https://doi.org/10.1093/nar/gkr606
29 https://doi.org/10.1101/gr.162339.113
30 https://doi.org/10.1126/science.1138140
31 https://doi.org/10.1126/science.1225829
32 https://doi.org/10.1126/science.1231143
33 https://doi.org/10.1126/science.1232033
34 https://doi.org/10.1126/science.1246981
35 https://doi.org/10.1126/science.1247005
36 https://doi.org/10.1371/journal.pone.0098186
37 https://doi.org/10.7554/elife.00471
38 schema:datePublished 2014-12
39 schema:datePublishedReg 2014-12-01
40 schema:description Components of the prokaryotic clustered, regularly interspaced, short palindromic repeats (CRISPR) loci have recently been repurposed for use in mammalian cells. The CRISPR-associated (Cas)9 can be programmed with a single guide RNA (sgRNA) to generate site-specific DNA breaks, but there are few known rules governing on-target efficacy of this system. We created a pool of sgRNAs, tiling across all possible target sites of a panel of six endogenous mouse and three endogenous human genes and quantitatively assessed their ability to produce null alleles of their target gene by antibody staining and flow cytometry. We discovered sequence features that improved activity, including a further optimization of the protospacer-adjacent motif (PAM) of Streptococcus pyogenes Cas9. The results from 1,841 sgRNAs were used to construct a predictive model of sgRNA activity to improve sgRNA design for gene editing and genetic screens. We provide an online tool for the design of highly active sgRNAs for any gene of interest.
41 schema:genre research_article
42 schema:inLanguage en
43 schema:isAccessibleForFree true
44 schema:isPartOf N8be27769453442e4803cf4b02fa4eb33
45 N8e0913e056164b8089d3b62c964e90d3
46 sg:journal.1115214
47 schema:name Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation
48 schema:pagination 1262-1267
49 schema:productId N54d7bc41d8c34b44a3173c737460e6b1
50 N55058e3e62bb4d8ea69f47c9ce409bea
51 N972e4b59b9ac40709183ec91df40ee4f
52 Nae8d2ce5f5c447e4997bab03f880e7e4
53 Ne16497478e4947ac826304834fe2c4d9
54 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033528408
55 https://doi.org/10.1038/nbt.3026
56 schema:sdDatePublished 2019-04-10T18:08
57 schema:sdLicense https://scigraph.springernature.com/explorer/license/
58 schema:sdPublisher N5aef07ebda8b4216a46ed74a8b76f0c2
59 schema:url http://www.nature.com/nbt/journal/v32/n12/full/nbt.3026.html
60 sgo:license sg:explorer/license/
61 sgo:sdDataset articles
62 rdf:type schema:ScholarlyArticle
63 N002b1582f3a4464bb318f10c7b906835 rdf:first sg:person.0603505234.56
64 rdf:rest Nccc263406feb47409579f55c509ba420
65 N05479a66d889422cbdc6ffa6df88ee62 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
66 schema:name Animals
67 rdf:type schema:DefinedTerm
68 N081b12f29c694496a42ffc1dc3db7436 rdf:first sg:person.0717130066.82
69 rdf:rest Na3d5bc3ea4ba48dfa9da5bb578fa628e
70 N0ad67a5aceee4a64b0848f297bcc4bfc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
71 schema:name Gene Targeting
72 rdf:type schema:DefinedTerm
73 N26a31af1554142b194eca5da3ef11443 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name RNA
75 rdf:type schema:DefinedTerm
76 N2abd88ff674141d199fb3ad3add9f012 rdf:first sg:person.01052352713.61
77 rdf:rest N081b12f29c694496a42ffc1dc3db7436
78 N4350860d3db54a5a83e5b438ff6e9807 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
79 schema:name CRISPR-Cas Systems
80 rdf:type schema:DefinedTerm
81 N43aa1a7c2bdd49c09fb6c6f35d6d9528 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
82 schema:name Mice
83 rdf:type schema:DefinedTerm
84 N54d7bc41d8c34b44a3173c737460e6b1 schema:name dimensions_id
85 schema:value pub.1033528408
86 rdf:type schema:PropertyValue
87 N55058e3e62bb4d8ea69f47c9ce409bea schema:name nlm_unique_id
88 schema:value 9604648
89 rdf:type schema:PropertyValue
90 N5aef07ebda8b4216a46ed74a8b76f0c2 schema:name Springer Nature - SN SciGraph project
91 rdf:type schema:Organization
92 N635476078e164ca890840db3bda156b4 rdf:first sg:person.01067500752.34
93 rdf:rest N2abd88ff674141d199fb3ad3add9f012
94 N74ec2a9ee295476d8a2f6451cb89ccf7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
95 schema:name Flow Cytometry
96 rdf:type schema:DefinedTerm
97 N7b0dff89bf28441b9d660e822fc32a53 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Gene Silencing
99 rdf:type schema:DefinedTerm
100 N8be27769453442e4803cf4b02fa4eb33 schema:issueNumber 12
101 rdf:type schema:PublicationIssue
102 N8e0913e056164b8089d3b62c964e90d3 schema:volumeNumber 32
103 rdf:type schema:PublicationVolume
104 N8f6dc923ca8b441aba9177e3ff1c0719 rdf:first sg:person.0753252352.23
105 rdf:rest Nb13f0429b57a4a76971a6052a85610ac
106 N972e4b59b9ac40709183ec91df40ee4f schema:name pubmed_id
107 schema:value 25184501
108 rdf:type schema:PropertyValue
109 Na3d5bc3ea4ba48dfa9da5bb578fa628e rdf:first sg:person.01270622506.69
110 rdf:rest rdf:nil
111 Nae8d2ce5f5c447e4997bab03f880e7e4 schema:name doi
112 schema:value 10.1038/nbt.3026
113 rdf:type schema:PropertyValue
114 Nb13f0429b57a4a76971a6052a85610ac rdf:first sg:person.01021365552.11
115 rdf:rest N635476078e164ca890840db3bda156b4
116 Nca40c7a4594e4657843ca9b9673c8ff3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
117 schema:name Humans
118 rdf:type schema:DefinedTerm
119 Ncbabcace4d094a939a160db1337c1139 rdf:first sg:person.01123503121.96
120 rdf:rest Ne0cb4fb53a9f4a519c2e17a1c67869fc
121 Nccc263406feb47409579f55c509ba420 rdf:first sg:person.01333575730.40
122 rdf:rest Ncbabcace4d094a939a160db1337c1139
123 Ne0cb4fb53a9f4a519c2e17a1c67869fc rdf:first sg:person.01223156657.41
124 rdf:rest N8f6dc923ca8b441aba9177e3ff1c0719
125 Ne16497478e4947ac826304834fe2c4d9 schema:name readcube_id
126 schema:value 9fb88c6042d089b73a95612380375076a25f49c042b160e63d94c95488362632
127 rdf:type schema:PropertyValue
128 Nf26102be0246456ca1541aefe3c38833 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Streptococcus pyogenes
130 rdf:type schema:DefinedTerm
131 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
132 schema:name Biological Sciences
133 rdf:type schema:DefinedTerm
134 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
135 schema:name Genetics
136 rdf:type schema:DefinedTerm
137 sg:grant.2439002 http://pending.schema.org/fundedItem sg:pub.10.1038/nbt.3026
138 rdf:type schema:MonetaryGrant
139 sg:grant.2682491 http://pending.schema.org/fundedItem sg:pub.10.1038/nbt.3026
140 rdf:type schema:MonetaryGrant
141 sg:grant.3493714 http://pending.schema.org/fundedItem sg:pub.10.1038/nbt.3026
142 rdf:type schema:MonetaryGrant
143 sg:journal.1115214 schema:issn 1087-0156
144 1546-1696
145 schema:name Nature Biotechnology
146 rdf:type schema:Periodical
147 sg:person.01021365552.11 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
148 schema:familyName Smith
149 schema:givenName Ian
150 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021365552.11
151 rdf:type schema:Person
152 sg:person.01052352713.61 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
153 schema:familyName Ebert
154 schema:givenName Benjamin L
155 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01052352713.61
156 rdf:type schema:Person
157 sg:person.01067500752.34 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
158 schema:familyName Sullender
159 schema:givenName Meagan
160 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01067500752.34
161 rdf:type schema:Person
162 sg:person.01123503121.96 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
163 schema:familyName Graham
164 schema:givenName Daniel B
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123503121.96
166 rdf:type schema:Person
167 sg:person.01223156657.41 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
168 schema:familyName Tothova
169 schema:givenName Zuzana
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223156657.41
171 rdf:type schema:Person
172 sg:person.01270622506.69 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
173 schema:familyName Root
174 schema:givenName David E
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01270622506.69
176 rdf:type schema:Person
177 sg:person.01333575730.40 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
178 schema:familyName Hartenian
179 schema:givenName Ella
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333575730.40
181 rdf:type schema:Person
182 sg:person.0603505234.56 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
183 schema:familyName Doench
184 schema:givenName John G
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0603505234.56
186 rdf:type schema:Person
187 sg:person.0717130066.82 schema:affiliation https://www.grid.ac/institutes/grid.38142.3c
188 schema:familyName Xavier
189 schema:givenName Ramnik J
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82
191 rdf:type schema:Person
192 sg:person.0753252352.23 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
193 schema:familyName Hegde
194 schema:givenName Mudra
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0753252352.23
196 rdf:type schema:Person
197 sg:pub.10.1038/nature09523 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009515358
198 https://doi.org/10.1038/nature09523
199 rdf:type schema:CreativeWork
200 sg:pub.10.1038/nature13166 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027499136
201 https://doi.org/10.1038/nature13166
202 rdf:type schema:CreativeWork
203 sg:pub.10.1038/nbt.2508 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019888616
204 https://doi.org/10.1038/nbt.2508
205 rdf:type schema:CreativeWork
206 sg:pub.10.1038/nbt.2623 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009511624
207 https://doi.org/10.1038/nbt.2623
208 rdf:type schema:CreativeWork
209 sg:pub.10.1038/nbt.2647 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012543463
210 https://doi.org/10.1038/nbt.2647
211 rdf:type schema:CreativeWork
212 sg:pub.10.1038/nbt.2800 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041802825
213 https://doi.org/10.1038/nbt.2800
214 rdf:type schema:CreativeWork
215 sg:pub.10.1038/nbt.2808 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048637524
216 https://doi.org/10.1038/nbt.2808
217 rdf:type schema:CreativeWork
218 sg:pub.10.1038/nbt.2889 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043519930
219 https://doi.org/10.1038/nbt.2889
220 rdf:type schema:CreativeWork
221 sg:pub.10.1038/nbt.2916 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043348902
222 https://doi.org/10.1038/nbt.2916
223 rdf:type schema:CreativeWork
224 sg:pub.10.1038/nbt936 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039709400
225 https://doi.org/10.1038/nbt936
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1016/j.cell.2013.08.022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034724285
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1016/j.molcel.2011.02.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043964993
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1073/pnas.0506580102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037705714
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1073/pnas.0810485105 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053380624
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1073/pnas.1109363108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012211256
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1093/nar/gkr606 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052438070
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1101/gr.162339.113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010306401
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1126/science.1138140 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036312168
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1126/science.1225829 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041850060
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1126/science.1231143 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019873131
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1126/science.1232033 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022072971
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1126/science.1246981 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043810806
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1126/science.1247005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007966801
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1371/journal.pone.0098186 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029929613
254 rdf:type schema:CreativeWork
255 https://doi.org/10.7554/elife.00471 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023633935
256 rdf:type schema:CreativeWork
257 https://www.grid.ac/institutes/grid.38142.3c schema:alternateName Harvard University
258 schema:name Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
259 Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
260 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
261 rdf:type schema:Organization
262 https://www.grid.ac/institutes/grid.66859.34 schema:alternateName Broad Institute
263 schema:name Brigham and Women's Hospital, Harvard Medical School, Department of Medicine, Division of Hematology, Boston, Massachusetts, USA.
264 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
265 rdf:type schema:Organization
 




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


...