Sequencer-Based Capillary Gel Electrophoresis (SCGE) Targeting the rDNA Internal Transcribed Spacer (ITS) Regions for Accurate Identification of Clinically Important Yeast Species
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{"title"=>"Sequencer-based capillary gel electrophoresis (scge) targeting the rDNA internal transcribed spacer (its) regions for accurate identification of clinically important yeast species", "type"=>"journal", "authors"=>[{"first_name"=>"Xin", "last_name"=>"Hou", "scopus_author_id"=>"56498365500"}, {"first_name"=>"Meng", "last_name"=>"Xiao", "scopus_author_id"=>"26868310100"}, {"first_name"=>"Sharon C.A.", "last_name"=>"Chen", "scopus_author_id"=>"7410259468"}, {"first_name"=>"He", "last_name"=>"Wang", "scopus_author_id"=>"55816287100"}, {"first_name"=>"Li", "last_name"=>"Zhang", "scopus_author_id"=>"55816281800"}, {"first_name"=>"Xin", "last_name"=>"Fan", "scopus_author_id"=>"55335031100"}, {"first_name"=>"Zhi Peng", "last_name"=>"Xu", "scopus_author_id"=>"56479427500"}, {"first_name"=>"Jing Wei", "last_name"=>"Cheng", "scopus_author_id"=>"56479572600"}, {"first_name"=>"Fanrong", "last_name"=>"Kong", "scopus_author_id"=>"7201838127"}, {"first_name"=>"Yu Pei", "last_name"=>"Zhao", "scopus_author_id"=>"7406635066"}, {"first_name"=>"Ying Chun", "last_name"=>"Xu", "scopus_author_id"=>"11840057200"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84977605433", "sgr"=>"84977605433", "doi"=>"10.1371/journal.pone.0154385", "pui"=>"611092718", "issn"=>"19326203"}, "id"=>"a6c65d75-1e35-3ebe-a834-5ecc5f4458d5", "link"=>"http://www.mendeley.com/research/sequencerbased-capillary-gel-electrophoresis-scge-targeting-rdna-internal-transcribed-spacer-regions-1", "reader_count"=>4, "reader_count_by_academic_status"=>{"Researcher"=>1, "Student > Ph. D. Student"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>1, "Student > Ph. D. Student"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>1}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/5004589"], "description"=>"<p>Fig 1A, structure of yeast ITS region and primers used in this study (showed in arrows with dashed lines). The duplex PCR using primers ITS1-FAM, ITS2 and ITS4 will theoretically generate two amplicons (for ITS1 and full-length ITS region, respectively). As the forward primer ITS1 was 5’-end FAM labeled, the amplicons can be observed by SCGE examination (peaks “a” and “b” in Fig 1B). B. an example of interpreting the SCGE results (strain 12HX414). Peaks “a” and “b” represent amplicons of ITS1 and full-length ITS region, respectively. As peak “a” and “a’” were separated by less than 1 bp, only peak “a” was counted (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154385#sec002\" target=\"_blank\">Methods</a> section).</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198433, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Principles_for_SCGE_ITS_length_types_LTs_identification_of_yeast_species_/3198433", "title"=>"Principles for SCGE ITS length types (LTs) identification of yeast species.", "pos_in_sequence"=>1, "defined_type"=>1, "published_date"=>"2016-04-22 06:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/5004634"], "description"=>"<p>The results of isolates collected from PUMCH in 2013 by SCGE.</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198466, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_results_of_isolates_collected_from_PUMCH_in_2013_by_SCGE_/3198466", "title"=>"The results of isolates collected from PUMCH in 2013 by SCGE.", "pos_in_sequence"=>6, "defined_type"=>3, "published_date"=>"2016-04-22 06:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/5004598"], "description"=>"<p>The amplicon sizes has been rounded up to the nearest whole number. Fig 2A, the whole database. Fig 2B, LTs of different species that had the same-length ITS1 or ITS region amplicons. In Fig 2A and 2B, gel-bands in blue or red represent amplicon of the ITS1 region, while gel-bands in purple or pink represent amplicon of the ITS region. Gel-bands in red or pink indicated the length of ITS1 or ITS amplicons were shared by different species.</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198442, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/SCGE_ITS_length_types_LTs_database_established_in_the_present_study_including_amplicon_lengths_bp_of_the_ITS1_and_ITS_regions_called_by_SCGE_for_each_LT_and_an_i_in_silico_i_gel_view_diagram_/3198442", "title"=>"SCGE ITS length types (LTs) database established in the present study, including amplicon lengths (bp) of the ITS1 and ITS regions called by SCGE for each LT, and an <i>in silico</i> gel-view diagram.", "pos_in_sequence"=>2, "defined_type"=>1, "published_date"=>"2016-04-22 06:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/5004643"], "description"=>"<p><i>In silico</i> analysis of 41 yeast species from GenBank not being involve in the ITS length type (LT) database.</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198475, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.t003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_i_In_silico_i_analysis_of_41_yeast_species_from_GenBank_not_being_involve_in_the_ITS_length_type_LT_database_/3198475", "title"=>"<i>In silico</i> analysis of 41 yeast species from GenBank not being involve in the ITS length type (LT) database.", "pos_in_sequence"=>7, "defined_type"=>3, "published_date"=>"2016-04-22 06:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/5004604"], "description"=>"<p>ITS length types (LTs) within <i>C</i>. <i>parapsilosis</i> species complex.</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198448, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/ITS_length_types_LTs_within_i_C_i_i_parapsilosis_i_species_complex_/3198448", "title"=>"ITS length types (LTs) within <i>C</i>. <i>parapsilosis</i> species complex.", "pos_in_sequence"=>3, "defined_type"=>1, "published_date"=>"2016-04-22 06:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/5004649"], "description"=>"<p>Comparison of SCGE, Vitek MS and ITS sequencing for identification of yeast species.</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198481, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.t004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparison_of_SCGE_Vitek_MS_and_ITS_sequencing_for_identification_of_yeast_species_/3198481", "title"=>"Comparison of SCGE, Vitek MS and ITS sequencing for identification of yeast species.", "pos_in_sequence"=>8, "defined_type"=>3, "published_date"=>"2016-04-22 06:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/5004613"], "description"=>"<p>Phylogenetic tree based on the ITS sequences of 41 ITS LT isolates and ITS LT ctr-3 is shown and was conducted using the maximum-likelihood method, using <i>Aspergillus niger</i> ATCC 16888T as an outgroup.</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198457, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenetic_tree_based_on_the_ITS_sequences_of_41_ITS_LT_isolates_and_ITS_LT_ctr_3_is_shown_and_was_conducted_using_the_maximum_likelihood_method_using_i_Aspergillus_niger_i_ATCC_16888T_as_an_outgroup_/3198457", "title"=>"Phylogenetic tree based on the ITS sequences of 41 ITS LT isolates and ITS LT ctr-3 is shown and was conducted using the maximum-likelihood method, using <i>Aspergillus niger</i> ATCC 16888T as an outgroup.", "pos_in_sequence"=>4, "defined_type"=>1, "published_date"=>"2016-04-22 06:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/5004622"], "description"=>"<p>Summarization of ITS1 and ITS sizes called by SCGE and DNA sequencing for five reference strains and 151 clinical isolates used for establishment of the SCGE ITS length type (LT) database.</p>", "links"=>[], "tags"=>["LT database", "SCGE", "32 species", "rDNA Internal Transcribed Spacer", "Trichosporon", "region length types", "silico analysis", "yeast species identification scheme"], "article_id"=>3198463, "categories"=>["Biochemistry", "Medicine", "Microbiology", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Sociology", "Biological Sciences not elsewhere classified"], "users"=>["Xin Hou", "Meng Xiao", "Sharon C.-A. Chen", "He Wang", "Li Zhang", "Xin Fan", "Zhi-Peng Xu", "Jing-Wei Cheng", "Fanrong Kong", "Yu-Pei Zhao", "Ying-Chun Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0154385.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Summarization_of_ITS1_and_ITS_sizes_called_by_SCGE_and_DNA_sequencing_for_five_reference_strains_and_151_clinical_isolates_used_for_establishment_of_the_SCGE_ITS_length_type_LT_database_/3198463", "title"=>"Summarization of ITS1 and ITS sizes called by SCGE and DNA sequencing for five reference strains and 151 clinical isolates used for establishment of the SCGE ITS length type (LT) database.", "pos_in_sequence"=>5, "defined_type"=>3, "published_date"=>"2016-04-22 06:26:32"}

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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