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Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

Publication Date: November 20, 2009
Journal: PLOS Genetics
Authors: Carol Soderlund, Anne Descour, Dave Kudrna, Matthew Bomhoff, et al
Volume: 5
Issue: 11
Pages: e1000740
DOI: http://doi.org/10.1371/journal.pgen.1000740
Publisher URL: http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1000740
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/19936069
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774520
Europe PMC: http://europepmc.org/abstract/MED/19936069
Web of Science: 000272419500035
Scopus: 73649094751
Mendeley: http://www.mendeley.com/research/sequencing-mapping-analysis-27455-maize-fulllength-cdnas

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{"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/ba745c31-66f6-4674-bfac-24efe96b1d93", "title"=>"Links to related papers", "body"=>"This article is part of the 2009 PLoS Genetics Maize Genome Collection. To view the whole collection, please visit \n<http://collections.plos.org/plosgenetics/maize.php>. For related papers in Science, please visit <http://www.sciencemag.org/cgi/content/short/326/5956/1071>", "highlightedText"=>"''maize genome''\nhttp://plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000740#article1.front1.article-meta1.abstract1.p1", "isRemoved"=>false, "created"=>"2009-11-24T16:03:24Z", "lastModified"=>"2009-11-24T16:03:24Z", "creator"=>{"userId"=>"131543"}, "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1000740", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2009-11-24T16:03:24Z", "replies"=>[]}

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{"files"=>["https://ndownloader.figshare.com/files/434017", "https://ndownloader.figshare.com/files/434058", "https://ndownloader.figshare.com/files/434093"], "description"=>"<div>Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5′ and 3′ UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (<a href=\"http://www.maizecdna.org\">www.maizecdna.org</a>).</div>", "links"=>[], "tags"=>["maize", "full-length", "cdnas"], "article_id"=>145628, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.s001", "https://dx.doi.org/10.1371/journal.pgen.1000740.s002", "https://dx.doi.org/10.1371/journal.pgen.1000740.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sequencing_Mapping_and_Analysis_of_27_455_Maize_Full_Length_cDNAs/145628", "title"=>"Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-11-20 01:33:48"}
{"files"=>["https://ndownloader.figshare.com/files/874673"], "description"=>"The 27k FLcDNAs were searched against annotated protein gene models of each species, and the overlapping matches between species are displayed in the Venn diagram. Two overlaps (25 overlapping hits between rice and poplar, and two overlapping hits between Arabidopsis and sorghum) are not listed.", "links"=>[], "tags"=>["genetics and genomics/bioinformatics", "genetics and genomics/gene discovery", "genetics and genomics/plant genomes and evolution"], "article_id"=>545109, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Homolog_analysis_with_rice_sorghum_Arabidopsis_and_poplar_/545109", "title"=>"Homolog analysis with rice, sorghum, Arabidopsis, and poplar.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:25:09"}
{"files"=>["https://ndownloader.figshare.com/files/874794"], "description"=>"The 24,354 FLcDNAs that mapped to a single locus were counted in 1Mb bins (number of FLcDNA/Mb), color-coded, and plotted on the maize chromosomes. The yellow indicates average density (∼12cDNAs/Mb), the red is higher than average, and the blue is lower. The brown-colored bars next to each chromosome represent the regions where FLcDNA density is higher than average +2 standard deviations ( = 32 FLcDNAs/Mb).", "links"=>[], "tags"=>["heat-map", "displayed", "maize"], "article_id"=>545241, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FLcDNA_density_heat_map_displayed_on_the_maize_chromosomes_/545241", "title"=>"FLcDNA density heat-map displayed on the maize chromosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:27:21"}
{"files"=>["https://ndownloader.figshare.com/files/874907"], "description"=>"Potential homeologous genes for the 24,354 single locus-mapped FLcDNAs were computed by using relaxed mapping parameters for aligning them to the maize genome. Approximately 44% SL-FLcDNAs had homeologous regions (ID; identity, AL; alignment length, SL; single locus, ML; multi loci (>4), 2–4L; 2–4 mapped loci).", "links"=>[], "tags"=>["homeologous", "genes", "maize"], "article_id"=>545357, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_homeologous_genes_in_the_maize_genome_/545357", "title"=>"Detection of homeologous genes in the maize genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:29:17"}
{"files"=>["https://ndownloader.figshare.com/files/875026"], "description"=>"(A) The red vertical lines indicate a mismatch with the consensus sequence, and green vertical lines indicate a gap in relation to the consensus sequence. The clone prefix indicates the project (BC – Yu, W – Wang, M – Messing, F – Feldman). (B) Base view of the 5′ ends of 7 FLcDNAs with alternative start sites in relation to the consensus sequence. This is a close-up of bases 97–164 from the alignment shown in (A). The red bases do not agree with the consensus.", "links"=>[], "tags"=>["contig", "69k", "snps"], "article_id"=>545473, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_contig_in_the_69k_loose_assembly_with_multiple_SNPs_and_GPs_/545473", "title"=>"A contig in the 69k loose assembly with multiple SNPs and GPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:31:13"}
{"files"=>["https://ndownloader.figshare.com/files/875179"], "description"=>"aReverse complemented clones (only allowed in the loose assembly).bSNPs and GPs (gap polymorphisms) were only identified in these contigs.cMany of these SNPs and GPs for the loose assembly are in the end regions.dPercentage of ends that are not the first/last two bases of the consensus sequence.ePercentage of clustered ends, where each cluster contains the ends within 10 bases of another.fPercentage of clusters ≥100 bases from the previous cluster (number of these that have at least 2 FLcDNAs in both clusters). The next three rows are the same but with different distances.", "links"=>[], "tags"=>["assembled"], "article_id"=>545625, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_assembled_contigs_/545625", "title"=>"Analysis of assembled contigs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:33:45"}
{"files"=>["https://ndownloader.figshare.com/files/875226"], "description"=>"aThe 69,306 downloaded FLcDNA sequences were further trimmed with our scripts, which removed some clones from the assembled set.bThe first letter of each project name is used to indicate if there was at least one FlcDNA from the project in the contig.cStrict assembly 1: 100% identity, ≤10 ignored end bases (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000740#s4\" target=\"_blank\">Materials and Methods</a>).dSemi-strict assembly 2: 90% identity, ≤15 ignored end bases.eLoose assembly 3: Reverse orientation, 80% identity, ≤350 ignored end bases.", "links"=>[], "tags"=>["maize", "flcdna"], "article_id"=>545675, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assemblies_of_four_maize_FLcDNA_projects_/545675", "title"=>"Assemblies of four maize FLcDNA projects.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:34:35"}
{"files"=>["https://ndownloader.figshare.com/files/875280"], "description"=>"Length of individual FLcDNA clones and assembled FLcDNA contigs.", "links"=>[], "tags"=>["flcdna", "clones", "assembled"], "article_id"=>545721, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Length_of_individual_FLcDNA_clones_and_assembled_FLcDNA_contigs_/545721", "title"=>"Length of individual FLcDNA clones and assembled FLcDNA contigs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:35:21"}
{"files"=>["https://ndownloader.figshare.com/files/875327"], "description"=>"Gene Ontology (GO) analysis of putative unique maize FLcDNAs.", "links"=>[], "tags"=>["ontology", "putative", "maize"], "article_id"=>545770, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_GO_analysis_of_putative_unique_maize_FLcDNAs_/545770", "title"=>"Gene Ontology (GO) analysis of putative unique maize FLcDNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:36:10"}
{"files"=>["https://ndownloader.figshare.com/files/875390"], "description"=>"aGao et al. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000740#pgen.1000740-Gao1\" target=\"_blank\">[27]</a>.bGuo et al. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000740#pgen.1000740-Guo2\" target=\"_blank\">[28]</a>.cPercent of 1,965 putative TFs identified from the maize FLcDNAs.dPercent of 2,383 TFs identified from the japonica rice annotated genes.ePercent of 1,922 TFs identified from the Arabidopsis annotated genes.", "links"=>[], "tags"=>["10", "putative", "transcription", "factors", "27k", "flcdna", "compared"], "article_id"=>545830, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_10_putative_transcription_factors_in_the_27k_FLcDNA_set_compared_with_rice_and_Arabidopsis_/545830", "title"=>"Top 10 putative transcription factors in the 27k FLcDNA set compared with rice and Arabidopsis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:37:10"}
{"files"=>["https://ndownloader.figshare.com/files/875437"], "description"=>"Top 10 GO Slim annotations and number of FLcDNAs.", "links"=>[], "tags"=>["10", "slim", "annotations"], "article_id"=>545880, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_10_GO_Slim_annotations_and_number_of_FLcDNAs_/545880", "title"=>"Top 10 GO Slim annotations and number of FLcDNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:38:00"}
{"files"=>["https://ndownloader.figshare.com/files/875483"], "description"=>"Summary of FLcDNA mapping to the maize genome.", "links"=>[], "tags"=>["flcdna", "maize"], "article_id"=>545925, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_FLcDNA_mapping_to_the_maize_genome_/545925", "title"=>"Summary of FLcDNA mapping to the maize genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:38:45"}
{"files"=>["https://ndownloader.figshare.com/files/875521"], "description"=>"aThese ESTs were sequenced as a preliminary project and were submitted to GenBank in 2002.", "links"=>[], "tags"=>["ests", "slippage"], "article_id"=>545970, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ZM_BF_ESTs_after_removal_of_slippage_and_poly_A_/545970", "title"=>"ZM_BF ESTs after removal of slippage and poly(A).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:39:30"}
{"files"=>["https://ndownloader.figshare.com/files/875564"], "description"=>"TE analysis of the 27k FLcDNAs.", "links"=>[], "tags"=>["27k"], "article_id"=>546016, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TE_analysis_of_the_27k_FLcDNAs_/546016", "title"=>"TE analysis of the 27k FLcDNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:40:16"}
{"files"=>["https://ndownloader.figshare.com/files/875606"], "description"=>"aNR = nucleotide repeat.", "links"=>[], "tags"=>["27k"], "article_id"=>546054, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SSR_analysis_of_the_27k_FLcDNAs_/546054", "title"=>"SSR analysis of the 27k FLcDNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:40:54"}
{"files"=>["https://ndownloader.figshare.com/files/875645"], "description"=>"aBold text highlight counts that are greater than the previous.", "links"=>[], "tags"=>["genetics and genomics/bioinformatics", "genetics and genomics/gene discovery", "genetics and genomics/plant genomes and evolution"], "article_id"=>546089, "categories"=>["Genetics"], "users"=>["Carol Soderlund", "Anne Descour", "Dave Kudrna", "Matthew Bomhoff", "Lomax Boyd", "Jennifer Currie", "Angelina Angelova", "Kristi Collura", "Marina Wissotski", "Elizabeth Ashley", "Darren Morrow", "John Fernandes", "Virginia Walbot", "Yeisoo Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000740.t011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Size_and_number_of_small_gaps_a_/546089", "title"=>"Size and number of small gapsa.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:41:29"}

PMC Usage Stats 362817 Apr 12:53 UTC

PMC Usage Stats | Further Information

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Relative Metric 51500012 Apr 19:34 UTC

Relative Metric

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F1000Prime25 Apr 10:25 UTC

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