Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion
Publication Date
March 02, 2017
Authors
Carlos Pulido Quetglas, Estel Aparicio Prat, Carme Arnan, Taisia Polidori, et al
Volume
13
Issue
3
Pages
e1005341
DOI
https://dx.plos.org/10.1371/journal.pcbi.1005341
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1005341
Scopus
85016774561
Mendeley
http://www.mendeley.com/research/scalable-design-paired-crispr-guide-rnas-genomic-deletion-1
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion", "type"=>"journal", "authors"=>[{"first_name"=>"Carlos", "last_name"=>"Pulido-Quetglas", "scopus_author_id"=>"57193803095"}, {"first_name"=>"Estel", "last_name"=>"Aparicio-Prat", "scopus_author_id"=>"36467975800"}, {"first_name"=>"Carme", "last_name"=>"Arnan", "scopus_author_id"=>"6506131325"}, {"first_name"=>"Taisia", "last_name"=>"Polidori", "scopus_author_id"=>"57190618064"}, {"first_name"=>"Toni", "last_name"=>"Hermoso", "scopus_author_id"=>"57193803795"}, {"first_name"=>"Emilio", "last_name"=>"Palumbo", "scopus_author_id"=>"56382801400"}, {"first_name"=>"Julia", "last_name"=>"Ponomarenko", "scopus_author_id"=>"57193495035"}, {"first_name"=>"Roderic", "last_name"=>"Guigo", "scopus_author_id"=>"7004339139"}, {"first_name"=>"Rory", "last_name"=>"Johnson", "scopus_author_id"=>"7407016005"}], "year"=>2017, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"15537358", "doi"=>"10.1371/journal.pcbi.1005341", "sgr"=>"85016774561", "scopus"=>"2-s2.0-85016774561", "isbn"=>"1111111111", "pmid"=>"28253259", "pui"=>"615171738"}, "id"=>"781162c6-81e1-362e-b8c4-57ae602ab220", "abstract"=>"CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.", "link"=>"http://www.mendeley.com/research/scalable-design-paired-crispr-guide-rnas-genomic-deletion-1", "reader_count"=>120, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>37, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>2, "Student > Master"=>14, "Other"=>8, "Student > Bachelor"=>11, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>37, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>2, "Student > Master"=>14, "Other"=>8, "Student > Bachelor"=>11, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Unspecified"=>6, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>43, "Agricultural and Biological Sciences"=>45, "Medicine and Dentistry"=>6, "Neuroscience"=>5, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Computer Science"=>4, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Neuroscience"=>{"Neuroscience"=>5}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>45}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>43}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"Argentina"=>1, "Sweden"=>1, "Belgium"=>1, "United States"=>2, "United Kingdom"=>1, "Australia"=>1, "Chile"=>1, "Portugal"=>1, "Spain"=>1}, "group_count"=>4}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85016774561"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85016774561?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85016774561&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=85016774561&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/85016774561", "dc:identifier"=>"SCOPUS_ID:85016774561", "eid"=>"2-s2.0-85016774561", "dc:title"=>"Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion", "dc:creator"=>"Pulido-Quetglas C.", "prism:publicationName"=>"PLoS Computational Biology", "prism:issn"=>"1553734X", "prism:eIssn"=>"15537358", "prism:volume"=>"13", "prism:issueIdentifier"=>"3", "prism:pageRange"=>nil, "prism:coverDate"=>"2017-03-01", "prism:coverDisplayDate"=>"March 2017", "prism:doi"=>"10.1371/journal.pcbi.1005341", "citedby-count"=>"19", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"Barcelona Institute of Science and Technology (BIST)", "affiliation-city"=>"Barcelona", "affiliation-country"=>"Spain"}, {"@_fa"=>"true", "affilname"=>"Universitat Pompeu Fabra Barcelona", "affiliation-city"=>"Barcelona", "affiliation-country"=>"Spain"}, {"@_fa"=>"true", "affilname"=>"Hospital del Mar", "affiliation-city"=>"Barcelona", "affiliation-country"=>"Spain"}], "pubmed-id"=>"28253259", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e1005341", "source-id"=>"4000151810", "openaccess"=>"1", "openaccessFlag"=>true}

Article Coverage Curated

Twitter

Counter

  • {"month"=>"3", "year"=>"2017", "pdf_views"=>"951", "xml_views"=>"15", "html_views"=>"4960"}
  • {"month"=>"4", "year"=>"2017", "pdf_views"=>"118", "xml_views"=>"3", "html_views"=>"655"}
  • {"month"=>"5", "year"=>"2017", "pdf_views"=>"92", "xml_views"=>"5", "html_views"=>"362"}
  • {"month"=>"6", "year"=>"2017", "pdf_views"=>"66", "xml_views"=>"1", "html_views"=>"297"}
  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"72", "xml_views"=>"3", "html_views"=>"277"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"85", "xml_views"=>"0", "html_views"=>"281"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"46", "xml_views"=>"1", "html_views"=>"199"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"47", "xml_views"=>"2", "html_views"=>"222"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"45", "xml_views"=>"0", "html_views"=>"179"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"88", "xml_views"=>"2", "html_views"=>"157"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"64", "xml_views"=>"1", "html_views"=>"144"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"38", "xml_views"=>"0", "html_views"=>"124"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"47", "xml_views"=>"0", "html_views"=>"131"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"42", "xml_views"=>"0", "html_views"=>"110"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"52", "xml_views"=>"0", "html_views"=>"135"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"56", "xml_views"=>"2", "html_views"=>"138"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"64", "xml_views"=>"4", "html_views"=>"150"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"31", "xml_views"=>"2", "html_views"=>"116"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"39", "xml_views"=>"1", "html_views"=>"97"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"32", "xml_views"=>"2", "html_views"=>"89"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"33", "xml_views"=>"0", "html_views"=>"111"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"46", "xml_views"=>"0", "html_views"=>"85"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"29", "xml_views"=>"0", "html_views"=>"113"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"30", "xml_views"=>"0", "html_views"=>"99"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"59", "xml_views"=>"3", "html_views"=>"108"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"29", "xml_views"=>"1", "html_views"=>"101"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"42", "xml_views"=>"0", "html_views"=>"81"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"72"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"22", "xml_views"=>"0", "html_views"=>"47"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"37", "xml_views"=>"0", "html_views"=>"68"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"23", "xml_views"=>"0", "html_views"=>"84"}
  • {"month"=>"10", "year"=>"2019", "pdf_views"=>"25", "xml_views"=>"0", "html_views"=>"59"}
  • {"month"=>"11", "year"=>"2019", "pdf_views"=>"31", "xml_views"=>"0", "html_views"=>"74"}
  • {"month"=>"12", "year"=>"2019", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"42"}
  • {"month"=>"1", "year"=>"2020", "pdf_views"=>"55", "xml_views"=>"1", "html_views"=>"74"}
  • {"month"=>"2", "year"=>"2020", "pdf_views"=>"27", "xml_views"=>"2", "html_views"=>"43"}
  • {"month"=>"3", "year"=>"2020", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"49"}
  • {"month"=>"4", "year"=>"2020", "pdf_views"=>"130", "xml_views"=>"0", "html_views"=>"57"}
  • {"month"=>"5", "year"=>"2020", "pdf_views"=>"79", "xml_views"=>"0", "html_views"=>"56"}
  • {"month"=>"6", "year"=>"2020", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"35"}
  • {"month"=>"7", "year"=>"2020", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"11"}

PMC Usage Stats

  • {"unique-ip"=>"61", "full-text"=>"50", "pdf"=>"24", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"61", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"46", "full-text"=>"41", "pdf"=>"22", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"41", "supp-data"=>"16", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"38", "full-text"=>"40", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"20", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"60", "full-text"=>"64", "pdf"=>"19", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"51", "supp-data"=>"12", "cited-by"=>"1", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"34", "full-text"=>"36", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"24", "supp-data"=>"22", "cited-by"=>"1", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"46", "full-text"=>"33", "pdf"=>"16", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"34", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"33", "full-text"=>"27", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"18", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"33", "full-text"=>"44", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"35", "supp-data"=>"21", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"31", "full-text"=>"28", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"26", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"20", "full-text"=>"22", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"17", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"34", "full-text"=>"35", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"26", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"39", "full-text"=>"33", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"40", "supp-data"=>"13", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"49", "full-text"=>"60", "pdf"=>"14", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"23", "supp-data"=>"4", "cited-by"=>"1", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"44", "full-text"=>"44", "pdf"=>"11", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"29", "supp-data"=>"3", "cited-by"=>"2", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"62", "full-text"=>"63", "pdf"=>"16", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"18", "supp-data"=>"5", "cited-by"=>"2", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"57", "full-text"=>"56", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"5", "cited-by"=>"1", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"63", "full-text"=>"63", "pdf"=>"13", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"13", "supp-data"=>"14", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"45", "full-text"=>"50", "pdf"=>"11", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"3", "cited-by"=>"1", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"26", "full-text"=>"22", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"4", "cited-by"=>"1", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"35", "full-text"=>"33", "pdf"=>"14", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"40", "full-text"=>"38", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"17", "cited-by"=>"1", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"44", "full-text"=>"35", "pdf"=>"10", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"5", "cited-by"=>"1", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"27", "full-text"=>"35", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"13", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"41", "full-text"=>"45", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"8", "cited-by"=>"1", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"59", "full-text"=>"64", "pdf"=>"12", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"12", "cited-by"=>"1", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"34", "full-text"=>"37", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"6", "cited-by"=>"1", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"46", "full-text"=>"49", "pdf"=>"10", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"11", "cited-by"=>"1", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"31", "full-text"=>"32", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"3", "cited-by"=>"1", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"39", "full-text"=>"42", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"4", "cited-by"=>"1", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"30", "full-text"=>"25", "pdf"=>"12", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"3", "cited-by"=>"1", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"49", "full-text"=>"55", "pdf"=>"13", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"3", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"37", "full-text"=>"42", "pdf"=>"13", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"3", "cited-by"=>"1", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"39", "full-text"=>"45", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"2", "cited-by"=>"1", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"34", "full-text"=>"47", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
Loading … Spinner
There are currently no alerts