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{"title"=>"Defined single-gene and multi-gene deletion mutant collections in salmonella enterica sv typhimurium", "type"=>"journal", "authors"=>[{"first_name"=>"Steffen", "last_name"=>"Porwollik", "scopus_author_id"=>"6603054994"}, {"first_name"=>"Carlos A.", "last_name"=>"Santiviago", "scopus_author_id"=>"6507214143"}, {"first_name"=>"Pui", "last_name"=>"Cheng", "scopus_author_id"=>"7401618999"}, {"first_name"=>"Fred", "last_name"=>"Long", "scopus_author_id"=>"24463663900"}, {"first_name"=>"Prerak", "last_name"=>"Desai", "scopus_author_id"=>"55203232500"}, {"first_name"=>"Jennifer", "last_name"=>"Fredlund", "scopus_author_id"=>"6602261792"}, {"first_name"=>"Shabarinath", "last_name"=>"Srikumar", "scopus_author_id"=>"36835927200"}, {"first_name"=>"Cecilia A.", "last_name"=>"Silva", "scopus_author_id"=>"24725707400"}, {"first_name"=>"Weiping", "last_name"=>"Chu", "scopus_author_id"=>"57198532994"}, {"first_name"=>"Xin", "last_name"=>"Chen", "scopus_author_id"=>"57134115800"}, {"first_name"=>"Rocío", "last_name"=>"Canals", "scopus_author_id"=>"6602188990"}, {"first_name"=>"M. Megan", "last_name"=>"Reynolds", "scopus_author_id"=>"57195268668"}, {"first_name"=>"Lydia", "last_name"=>"Bogomolnaya", "scopus_author_id"=>"13604685300"}, {"first_name"=>"Christine", "last_name"=>"Shields", "scopus_author_id"=>"55909985900"}, {"first_name"=>"Ping", "last_name"=>"Cui", "scopus_author_id"=>"55831663500"}, {"first_name"=>"Jinbai", "last_name"=>"Guo", "scopus_author_id"=>"7404488878"}, {"first_name"=>"Yi", "last_name"=>"Zheng", "scopus_author_id"=>"57198813530"}, {"first_name"=>"Tiana", "last_name"=>"Endicott-Yazdani", "scopus_author_id"=>"55910174300"}, {"first_name"=>"Hee Jeong", "last_name"=>"Yang", "scopus_author_id"=>"22956268500"}, {"first_name"=>"Aimee", "last_name"=>"Maple", "scopus_author_id"=>"55910285000"}, {"first_name"=>"Yury", "last_name"=>"Ragoza", "scopus_author_id"=>"55910116100"}, {"first_name"=>"Carlos J.", "last_name"=>"Blondel", "scopus_author_id"=>"22936642500"}, {"first_name"=>"Camila", "last_name"=>"Valenzuela", "scopus_author_id"=>"37666086900"}, {"first_name"=>"Helene", "last_name"=>"Andrews-Polymenis", "scopus_author_id"=>"9737261400"}, {"first_name"=>"Michael", "last_name"=>"McClelland", "scopus_author_id"=>"7103047213"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"373506533", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0099820", "scopus"=>"2-s2.0-84904133867", "pmid"=>"25007190", "sgr"=>"84904133867"}, "id"=>"f7da52da-a487-311e-a1a6-dd439c881ea9", "abstract"=>"We constructed two collections of targeted single gene deletion (SGD) mutants and two collections of targeted multi-gene deletion (MGD) mutants in Salmonella enterica sv Typhimurium 14028s. The SGD mutant collections contain (1), 3517 mutants in which a single gene is replaced by a cassette containing a kanamycin resistance (KanR) gene oriented in the sense direction (SGD-K), and (2), 3376 mutants with a chloramphenicol resistance gene (CamR) oriented in the antisense direction (SGD-C). A combined total of 3773 individual genes were deleted across these SGD collections. The MGD collections contain mutants bearing deletions of contiguous regions of three or more genes and include (3), 198 mutants spanning 2543 genes replaced by a KanR cassette (MGD-K), and (4), 251 mutants spanning 2799 genes replaced by a CamR cassette (MGD-C). Overall, 3476 genes were deleted in at least one MGD collection. The collections with different antibiotic markers permit construction of all viable combinations of mutants in the same background. Together, the libraries allow hierarchical screening of MGDs for different phenotypic followed by screening of SGDs within the target MGD regions. The mutants of these collections are stored at BEI Resources (www.beiresources.org) and publicly available.", "link"=>"http://www.mendeley.com/research/defined-singlegene-multigene-deletion-mutant-collections-salmonella-enterica-sv-typhimurium", "reader_count"=>48, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>7, "Student > Bachelor"=>5, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>7, "Student > Bachelor"=>5, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>23, "Arts and Humanities"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>7}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Sudan"=>1, "South Africa"=>1, "Italy"=>1, "France"=>1, "Indonesia"=>1}, "group_count"=>4}

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• http://doi.org/10.1371/journal.pone.0225131
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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/c8d61d03-a11c-4f20-8a5f-391a1080e1cb", "title"=>"Updated table of mutants", "body"=>"We occasionally upload the list of mutants as we learn more about them. Contact us for the most recent list.", "isRemoved"=>false, "created"=>"2015-07-22T18:56:30Z", "lastModified"=>"2015-07-22T18:56:30Z", "creator"=>{"userId"=>"515512"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"Author"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0099820", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2015-07-22T18:56:30Z", "replies"=>[]}

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• {"id"=>"487270681168859136", "text"=>"Congratulations @drdrAatBLC, our @plosone paper on SGD and MGD mutant collections in Salmonella Typhimurium is out!!! http://t.co/RaH96rvaQA", "created_at"=>"2014-07-10T16:22:38Z", "user"=>"_Dr_cLiFf_", "user_name"=>"eL cLiFf", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000458613634/02c98257dfadd2d966efcee58cccf82c_normal.jpeg"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1585874"], "description"=>"<p>A. General procedure and logistics of mutant generation, storage and characterization. B. Identification of obtained mutants and mapping of mutants to specific wells by a “Hypercube” Combinatorial Pooling approach, essentially as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099820#pone.0099820-Goodman1\" target=\"_blank\">[30]</a>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "genetics", "Gene identification and analysis", "Genetic screens", "microbiology", "Medical microbiology", "Microbial pathogens", "Bacterial pathogens", "Salmonella", "Gastroenterology and hepatology", "Bacterial and foodborne illness", "Infectious diseases", "Foodborne diseases"], "article_id"=>1098013, "categories"=>["Biological Sciences"], "users"=>["Steffen Porwollik", "Carlos A. Santiviago", "Pui Cheng", "Fred Long", "Prerak Desai", "Jennifer Fredlund", "Shabarinath Srikumar", "Cecilia A. Silva", "Weiping Chu", "Xin Chen", "Rocío Canals", "M. Megan Reynolds", "Lydia Bogomolnaya", "Christine Shields", "Ping Cui", "Jinbai Guo", "Yi Zheng", "Tiana Endicott-Yazdani", "Hee-Jeong Yang", "Aimee Maple", "Yury Ragoza", "Carlos J. Blondel", "Camila Valenzuela", "Helene Andrews-Polymenis", "Michael McClelland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099820.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Workflow_of_collection_construction_and_verification_/1098013", "title"=>"Workflow of collection construction and verification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-09 03:03:57"}
• {"files"=>["https://ndownloader.figshare.com/files/1585875"], "description"=>"a<p>CDS where no transposon insertion was found in a high complexity random transposon library <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099820#pone.0099820-Canals1\" target=\"_blank\">[29]</a>. List of mutants present in our collections. All <i>S</i>. Typhimurium strain 14028s annotated features <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099820#pone.0099820-Jarvik1\" target=\"_blank\">[12]</a> are presented along with their status in our single-gene deletion (SGD) mutant collections. Corresponding genes in <i>S</i>. Typhimurium strain LT2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099820#pone.0099820-McClelland1\" target=\"_blank\">[27]</a> that have at least 70% DNA identity and at least 70% coverage are annotated. The SGD collections are listed in genome order, followed by the multi-gene deletion (MGD) collections in genome order. For MGDs, only those primer pairs that resulted in successful deletion in at least one of the two varieties (Kan or Cam) are shown. Primer sequences, their genome locations, and the results of mutant generation, verification, and mapping to 96-well plates are shown. Empty wells are not listed.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "genetics", "Gene identification and analysis", "Genetic screens", "microbiology", "Medical microbiology", "Microbial pathogens", "Bacterial pathogens", "Salmonella", "Gastroenterology and hepatology", "Bacterial and foodborne illness", "Infectious diseases", "Foodborne diseases"], "article_id"=>1098014, "categories"=>["Biological Sciences"], "users"=>["Steffen Porwollik", "Carlos A. Santiviago", "Pui Cheng", "Fred Long", "Prerak Desai", "Jennifer Fredlund", "Shabarinath Srikumar", "Cecilia A. Silva", "Weiping Chu", "Xin Chen", "Rocío Canals", "M. Megan Reynolds", "Lydia Bogomolnaya", "Christine Shields", "Ping Cui", "Jinbai Guo", "Yi Zheng", "Tiana Endicott-Yazdani", "Hee-Jeong Yang", "Aimee Maple", "Yury Ragoza", "Carlos J. Blondel", "Camila Valenzuela", "Helene Andrews-Polymenis", "Michael McClelland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099820.t001", "stats"=>{"downloads"=>2, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_collection_statistics_/1098014", "title"=>"Summary of collection statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-09 03:03:57"}
• {"files"=>["https://ndownloader.figshare.com/files/1585885"], "description"=>"<div><p>We constructed two collections of targeted single gene deletion (SGD) mutants and two collections of targeted multi-gene deletion (MGD) mutants in <i>Salmonella enterica</i> sv Typhimurium 14028s. The SGD mutant collections contain (1), 3517 mutants in which a single gene is replaced by a cassette containing a kanamycin resistance (Kan^R) gene oriented in the sense direction (SGD-K), and (2), 3376 mutants with a chloramphenicol resistance gene (Cam^R) oriented in the antisense direction (SGD-C). A combined total of 3773 individual genes were deleted across these SGD collections. The MGD collections contain mutants bearing deletions of contiguous regions of three or more genes and include (3), 198 mutants spanning 2543 genes replaced by a Kan^R cassette (MGD-K), and (4), 251 mutants spanning 2799 genes replaced by a Cam^R cassette (MGD-C). Overall, 3476 genes were deleted in at least one MGD collection. The collections with different antibiotic markers permit construction of all viable combinations of mutants in the same background. Together, the libraries allow hierarchical screening of MGDs for different phenotypic followed by screening of SGDs within the target MGD regions. The mutants of these collections are stored at BEI Resources (<a href=\"http://www.beiresources.org\" target=\"_blank\">www.beiresources.org</a>) and publicly available.</p></div>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "genetics", "Gene identification and analysis", "Genetic screens", "microbiology", "Medical microbiology", "Microbial pathogens", "Bacterial pathogens", "Salmonella", "Gastroenterology and hepatology", "Bacterial and foodborne illness", "Infectious diseases", "Foodborne diseases", "defined", "single-gene", "multi-gene", "deletion", "mutant", "collections", "sv", "typhimurium"], "article_id"=>1098022, "categories"=>["Biological Sciences"], "users"=>["Steffen Porwollik", "Carlos A. Santiviago", "Pui Cheng", "Fred Long", "Prerak Desai", "Jennifer Fredlund", "Shabarinath Srikumar", "Cecilia A. Silva", "Weiping Chu", "Xin Chen", "Rocío Canals", "M. Megan Reynolds", "Lydia Bogomolnaya", "Christine Shields", "Ping Cui", "Jinbai Guo", "Yi Zheng", "Tiana Endicott-Yazdani", "Hee-Jeong Yang", "Aimee Maple", "Yury Ragoza", "Carlos J. Blondel", "Camila Valenzuela", "Helene Andrews-Polymenis", "Michael McClelland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099820", "stats"=>{"downloads"=>11, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Defined_Single_Gene_and_Multi_Gene_Deletion_Mutant_Collections_in_Salmonella_enterica_sv_Typhimurium/1098022", "title"=>"Defined Single-Gene and Multi-Gene Deletion Mutant Collections in <i>Salmonella enterica</i> sv Typhimurium", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-09 03:03:57"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[333]}, {"subject_area"=>"/Biology and life sciences/Microbiology", "average_usage"=>[317]}, {"subject_area"=>"/Medicine and health sciences/Infectious diseases", "average_usage"=>[319]}]}

F1000Prime