A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni
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{"title"=>"A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni", "type"=>"journal", "authors"=>[{"first_name"=>"Anna V.", "last_name"=>"Protasio", "scopus_author_id"=>"24576822700"}, {"first_name"=>"Isheng J.", "last_name"=>"Tsai", "scopus_author_id"=>"36054156300"}, {"first_name"=>"Anne", "last_name"=>"Babbage", "scopus_author_id"=>"6506774044"}, {"first_name"=>"Sarah", "last_name"=>"Nichol", "scopus_author_id"=>"54950988300"}, {"first_name"=>"Martin", "last_name"=>"Hunt", "scopus_author_id"=>"50061142000"}, {"first_name"=>"Martin A.", "last_name"=>"Aslett", "scopus_author_id"=>"56137050400"}, {"first_name"=>"Nishadi", "last_name"=>"de Silva", "scopus_author_id"=>"56355921100"}, {"first_name"=>"Giles S.", "last_name"=>"Velarde", "scopus_author_id"=>"6701654325"}, {"first_name"=>"Tim J.C.", "last_name"=>"Anderson", "scopus_author_id"=>"25635409900"}, {"first_name"=>"Richard C.", "last_name"=>"Clark", "scopus_author_id"=>"55473895000"}, {"first_name"=>"Claire", "last_name"=>"Davidson", "scopus_author_id"=>"35788750800"}, {"first_name"=>"Gary P.", "last_name"=>"Dillon", "scopus_author_id"=>"7007048394"}, {"first_name"=>"Nancy E.", "last_name"=>"Holroyd", "scopus_author_id"=>"15047970900"}, {"first_name"=>"Philip T.", "last_name"=>"LoVerde", "scopus_author_id"=>"7005559278"}, {"first_name"=>"Christine", "last_name"=>"Lloyd", "scopus_author_id"=>"7202193194"}, {"first_name"=>"Jacquelline", "last_name"=>"McQuillan", "scopus_author_id"=>"35741312300"}, {"first_name"=>"Guilherme", "last_name"=>"Oliveira", "scopus_author_id"=>"56267565400"}, {"first_name"=>"Thomas D.", "last_name"=>"Otto", "scopus_author_id"=>"7103379081"}, {"first_name"=>"Sophia J.", "last_name"=>"Parker-Manuel", "scopus_author_id"=>"49862120500"}, {"first_name"=>"Michael A.", "last_name"=>"Quail", "scopus_author_id"=>"35380885000"}, {"first_name"=>"R. Alan", "last_name"=>"Wilson", "scopus_author_id"=>"55605775488"}, {"first_name"=>"Adhemar", "last_name"=>"Zerlotini", "scopus_author_id"=>"16837528100"}, {"first_name"=>"David W.", "last_name"=>"Dunne", "scopus_author_id"=>"35449214800"}, {"first_name"=>"Matthew", "last_name"=>"Berriman", "scopus_author_id"=>"6701402385"}], "year"=>2012, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"pui"=>"364192324", "sgr"=>"84856579279", "issn"=>"19352727", "pmid"=>"22253936", "scopus"=>"2-s2.0-84856579279", "doi"=>"10.1371/journal.pntd.0001455", "isbn"=>"1935-2735 (Electronic)\\r1935-2727 (Linking)"}, "id"=>"6b1d92ae-1342-32d9-bc1e-846538832322", "abstract"=>"Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people in developing countries. Amongst the human-infective species, Schistosoma mansoni is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome. We used Sanger capillary and deep-coverage Illumina sequencing from clonal worms to upgrade the highly fragmented draft 380 Mb genome to one with only 885 scaffolds and more than 81% of the bases organised into chromosomes. We have also used transcriptome sequencing (RNA-seq) from four time points in the parasite's life cycle to refine gene predictions and profile their expression. More than 45% of predicted genes have been extensively modified and the total number has been reduced from 11,807 to 10,852. Using the new version of the genome, we identified trans-splicing events occurring in at least 11% of genes and identified clear cases where it is used to resolve polycistronic transcripts. We have produced a high-resolution map of temporal changes in expression for 9,535 genes, covering an unprecedented dynamic range for this organism. All of these data have been consolidated into a searchable format within the GeneDB (www.genedb.org) and SchistoDB (www.schistodb.net) databases. With further transcriptional profiling and genome sequencing increasingly accessible, the upgraded genome will form a fundamental dataset to underpin further advances in schistosome research.", "link"=>"http://www.mendeley.com/research/systematically-improved-high-quality-genome-transcriptome-human-blood-fluke-schistosoma-mansoni", "reader_count"=>106, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>9, "Researcher"=>25, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>6, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>16, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>9, "Researcher"=>25, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>6, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>16, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Agricultural and Biological Sciences"=>66, "Veterinary Science and Veterinary Medicine"=>1, "Business, Management and Accounting"=>2, "Chemistry"=>4, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Medicine and Dentistry"=>6, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Psychology"=>1, "Social Sciences"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Social Sciences"=>{"Social Sciences"=>2}, "Psychology"=>{"Psychology"=>1}, "Unspecified"=>{"Unspecified"=>8}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>66}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Uruguay"=>2, "Egypt"=>1, "Brazil"=>3, "United Kingdom"=>2, "Israel"=>1, "Switzerland"=>1, "Russia"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/694248"], "description"=>"<p>(A) Generation of clonal adult worms for Illumina sequencing. A single <i>B. glabrata</i> snail was infected with one miracidum only. The normal asexual reproduction stage of the sporocyst in the snail produces thousands of clonal cercariae that were used to infect mice. Clonal adult worms were recovered 7 weeks post-infection and processed for DNA extraction. (B) Closing gaps with IMAGE. Illumina data generated from the clonal adult worms were used to close gaps in the assembly using IMAGE <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Tsai1\" target=\"_blank\">[7]</a> and, in conjunction with previous sequencing data, linkage markers and BAC ends, allowed the genome to be assembled into chromosomes. (C) Organisation of the <i>S. mansoni</i> genome into chromosomes. Top: The total length of the scaffolds that have evidence (either linkage markers or FISH-mapped BACs) assigning them to the 7 autosomal and W/Z chromosomes. Bottom: A schematic diagram showing the example of supercontig_21 (3 Mb), which was allocated to chromosome 6 using information from genetic mapping <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Criscione1\" target=\"_blank\">[17]</a>, and was able to link together 9 supercontigs from the old assembly into the first 350 kb.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>364653, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Improving_the_genome_assembly_of_S_mansoni_/364653", "title"=>"Improving the genome assembly of S. mansoni.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-10 01:17:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/695120"], "description"=>"<p>Figures refer to those genes with significant differential expression (adjusted p-value<0.01). NB the v5.0 assembly contains 10,852 genes.</p>", "links"=>[], "tags"=>["differentially"], "article_id"=>365515, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.t004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_differentially_expressed_genes_/365515", "title"=>"Number of differentially expressed genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-10 01:31:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/695306"], "description"=>"<p>Number of RNA-seq reads mapped using SSAHA2 to the genome from libraries prepared from cercariae (Cerc); 3-hour post-infection schistosomula (3 h Som); 24-hour post-infection schistosomula (24 h Som); and mixed male and female adult worms (Adult).</p>a<p>reads mapped within expected distance apart and in the correct orientation.</p>b<p>reads that were properly mapped to the new assembly but not in the previous.</p>", "links"=>[], "tags"=>["rna-seq"], "article_id"=>365705, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_RNA_seq_mapping_/365705", "title"=>"Summary of RNA-seq mapping.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-10 01:35:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/694511"], "description"=>"<p>(A) Heatmap displaying comparisons between previous gene models and transcript fragments generated from Cufflinks. For each model, the extent of coding region that overlaps with a Cufflinks' model and the proportion of correctly predicted exon boundaries was calculated and categorised into bins of 70–100%. Models in this plot were excluded with less than 70% of their exon boundaries or coding regions predicted. (B), (C) and (D) Example scenarios of Cufflinks' models compared with previous gene models where (B) the Cufflinks prediction is identical to the 1,239 existing models; (C) Cufflinks fails to identify small introns; (D) Cufflinks removes incorrect introns present in the previous gene model, probably due to the improved assembly which, by correcting gaps, produced a longer single exon while the reading frame is preserved.</p>", "links"=>[], "tags"=>["annotation"], "article_id"=>364917, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.g003", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Improvement_of_gene_annotation_using_RNA_seq_/364917", "title"=>"Improvement of gene annotation using RNA-seq.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-10 01:21:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/353149", "https://ndownloader.figshare.com/files/353183", "https://ndownloader.figshare.com/files/353232", "https://ndownloader.figshare.com/files/353274", "https://ndownloader.figshare.com/files/353318", "https://ndownloader.figshare.com/files/353355", "https://ndownloader.figshare.com/files/353391", "https://ndownloader.figshare.com/files/353411", "https://ndownloader.figshare.com/files/353440", "https://ndownloader.figshare.com/files/353474", "https://ndownloader.figshare.com/files/353487", "https://ndownloader.figshare.com/files/353499", "https://ndownloader.figshare.com/files/353517", "https://ndownloader.figshare.com/files/353531"], "description"=>"<div><p>Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people in developing countries. Amongst the human-infective species, <em>Schistosoma mansoni</em> is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome. We used Sanger capillary and deep-coverage Illumina sequencing from clonal worms to upgrade the highly fragmented draft 380 Mb genome to one with only 885 scaffolds and more than 81% of the bases organised into chromosomes. We have also used transcriptome sequencing (RNA-seq) from four time points in the parasite's life cycle to refine gene predictions and profile their expression. More than 45% of predicted genes have been extensively modified and the total number has been reduced from 11,807 to 10,852. Using the new version of the genome, we identified <em>trans</em>-splicing events occurring in at least 11% of genes and identified clear cases where it is used to resolve polycistronic transcripts. We have produced a high-resolution map of temporal changes in expression for 9,535 genes, covering an unprecedented dynamic range for this organism. All of these data have been consolidated into a searchable format within the GeneDB (<a href=\"http://www.genedb.org\">www.genedb.org</a>) and SchistoDB (<a href=\"http://www.schistodb.net\">www.schistodb.net</a>) databases. With further transcriptional profiling and genome sequencing increasingly accessible, the upgraded genome will form a fundamental dataset to underpin further advances in schistosome research.</p> </div>", "links"=>[], "tags"=>["systematically", "genome", "transcriptome", "fluke"], "article_id"=>129798, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001455.s001", "https://dx.doi.org/10.1371/journal.pntd.0001455.s002", "https://dx.doi.org/10.1371/journal.pntd.0001455.s003", "https://dx.doi.org/10.1371/journal.pntd.0001455.s004", "https://dx.doi.org/10.1371/journal.pntd.0001455.s005", "https://dx.doi.org/10.1371/journal.pntd.0001455.s006", "https://dx.doi.org/10.1371/journal.pntd.0001455.s007", "https://dx.doi.org/10.1371/journal.pntd.0001455.s008", "https://dx.doi.org/10.1371/journal.pntd.0001455.s009", "https://dx.doi.org/10.1371/journal.pntd.0001455.s010", "https://dx.doi.org/10.1371/journal.pntd.0001455.s011", "https://dx.doi.org/10.1371/journal.pntd.0001455.s012", "https://dx.doi.org/10.1371/journal.pntd.0001455.s013", "https://dx.doi.org/10.1371/journal.pntd.0001455.s014"], "stats"=>{"downloads"=>28, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Systematically_Improved_High_Quality_Genome_and_Transcriptome_of_the_Human_Blood_Fluke_Schistosoma_mansoni_/129798", "title"=>"A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke <em>Schistosoma mansoni</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-01-10 02:43:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/694996"], "description"=>"<p>Venn diagram represents the distribution of genes above 95 percentile of expression in 3 different life cycle stages of the parasite. Examples of the genes/processes found within these groups are discussed in the main text.</p>", "links"=>[], "tags"=>["95", "percentile", "cercariae", "intra-mammalian"], "article_id"=>365379, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.g007", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_with_expression_above_the_95_percentile_different_in_cercariae_and_intra_mammalian_stages_/365379", "title"=>"Genes with expression above the 95 percentile different in cercariae and intra-mammalian stages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-10 01:29:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/694771"], "description"=>"<p>Barplots represent relative normalized reads (from RNA-seq data) for 3 transcripts, asterisks represent comparisons where differential expression is significant (adjusted p-value<0.01). Relative expression reported in the literature <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Ram1\" target=\"_blank\">[46]</a>, <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Neumann1\" target=\"_blank\">[49]</a>, <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Stein1\" target=\"_blank\">[51]</a> is shown at the bottom (+++, high expression, ++ medium expression, + some expression, − not expressed, NA no information available). C = cercariae, 3S = 3-hour schistosomula, 24S = 24-hour schistosomula, A = adult.</p>", "links"=>[], "tags"=>["genes", "developmentally"], "article_id"=>365167, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.g005", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_expression_of_genes_previously_identified_to_be_developmentally_regulated_/365167", "title"=>"Comparison of expression of genes previously identified to be developmentally regulated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-10 01:26:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/695248"], "description"=>"<p>The criteria for including genes into each category are described in the main text.</p>a<p>Version 4.0.</p>b<p>Version 5.0.</p>", "links"=>[], "tags"=>["genetics and genomics"], "article_id"=>365643, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.t003", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fate_of_gene_models_/365643", "title"=>"Fate of gene models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-10 01:34:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/694875"], "description"=>"<p>The plot (left) shows the log fold change (y-axis) vs. log relative concentration (x-axis) for the cercariae – 3-hour schistosomula comparison. A total of 1,518 genes are differentially expressed between these two life cycles stages (adjusted p-value<0.01). On the right, example coverage plots for differentially and non-differentially expressed genes. Of particular interest, genes up regulated in the 3-hour schistosomula stage are enriched in G-protein coupled receptors and integrins, suggesting that signalling is a key process in this life-cycle transition.</p>", "links"=>[], "tags"=>["differentially"], "article_id"=>365273, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.g006", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_differentially_expressed_genes_/365273", "title"=>"Detection of differentially expressed genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-10 01:27:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/694375"], "description"=>"<p>Gene models were migrated from previous version using RATT <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Otto1\" target=\"_blank\">[22]</a>. Repeats and sequencing errors in the old assembly resulted in ambiguities and sequences being represented more than once. In the new version, many scaffolds coalesced into one region and hence the gene models contained in them overlap each other. In this example, four supercontigs from the previous version collapsed on an unplaced region of Chromosome 3 in the new assembly. The smaller gene models are now obsolete as they were clearly incomplete annotations and their coding region are part of the exons of the larger gene model.</p>", "links"=>[], "tags"=>["redundancies", "produces"], "article_id"=>364771, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Removal_of_assembly_redundancies_produces_a_more_reliable_set_of_gene_models_/364771", "title"=>"Removal of assembly redundancies produces a more reliable set of gene models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-10 01:19:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/695182"], "description"=>"a<p>Version 4.0 of the <i>S. mansoni</i> genome was the published draft genome <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Berriman1\" target=\"_blank\">[3]</a>. Note the sequence in version v4.0 was identical to the previously released v3.1.</p>b<p>Version 5.0.</p>c<p>This figure refers to a “super-scaffold” of chromosome I sequence where 41 assembly-scaffolds are linked using genetic markers.</p>d<p>101,079,940 pairs of Illumina reads.</p>e<p>Reads mapped in their correct orientation and at a distance apart that corresponds to that predicted by the fragment library size.</p>f<p>Reads that mapped in their correct orientation but at a distance apart that did not match that predicted by the fragment library size.</p>", "links"=>[], "tags"=>["schistosoma", "mansoni", "genome"], "article_id"=>365574, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_old_and_improved_Schistosoma_mansoni_genome_assemblies_/365574", "title"=>"Characteristics of the old and improved Schistosoma mansoni genome assemblies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-10 01:32:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/694618"], "description"=>"<p>(A) Schematic view of the 5′ end of <i>trans</i>-spliced gene Smp_176420. Shaded coverage plots represent non-normalized RNA-seq reads still containing the spliced-leader (SL) sequence (green – unclipped reads) and reads previously found to contain the SL sequence (orange - clipped). In the latter, the SL sequence was removed prior to aligning the reads to the genome; which improved the reads mapability (lower in the unclipped reads than in the orange reads). (B) RT-PCR validation of 10 putative trans-spliced genes with SL1 as forward primer and a gene-specific reverse primer. Smp_024110.1, previously described as trans-spliced <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Davis1\" target=\"_blank\">[41]</a>, was included as a positive control (indicated with ‘+’) while Smp_045200.1 was included as a negative control (‘−’). All PCRs but one (Smp_176590.1) show bands corresponding to expected PCR product size. (C) Schematic view of the putative polycistron Smp_079750-Smp_079760. PCR1 represents the amplicon obtained from the unprocessed polycistronic transcript containing the intergenic region while PCR2 the trans-spliced form of Smp_079760. (D) RT-PCR validation of 5 putative polycistrons and a positive control (Smp_024110-Smp_024120; lane 9) previously reported in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001455#pntd.0001455-Davis2\" target=\"_blank\">[45]</a>. Each putative polycistron was subjected to two PCRs that correspond to PCR1 (e.g lane 1) and PCR2 (e.g lane 2) in panel C.</p>", "links"=>[], "tags"=>["reveals", "trans-spliced"], "article_id"=>365017, "categories"=>["Genetics"], "users"=>["Anna V. Protasio", "Isheng J. Tsai", "Anne Babbage", "Sarah Nichol", "Martin Hunt", "Martin A. Aslett", "Nishadi De Silva", "Giles S. Velarde", "Tim J. C. Anderson", "Richard C. Clark", "Claire Davidson", "Gary P. Dillon", "Nancy E. Holroyd", "Philip T. LoVerde", "Christine Lloyd", "Jacquelline McQuillan", "Guilherme Oliveira", "Thomas D. Otto", "Sophia J. Parker-Manuel", "Michael A. Quail", "R. Alan Wilson", "Adhemar Zerlotini", "David W. Dunne", "Matthew Berriman"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001455.g004", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RNA_seq_reveals_trans_spliced_transcripts_/365017", "title"=>"RNA-seq reveals trans-spliced transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-10 01:23:37"}

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  • {"unique-ip"=>"25", "full-text"=>"28", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"25", "full-text"=>"21", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[333, 576, 707, 814, 908, 1004, 1104, 1197, 1280, 1370, 1449, 1531, 1603, 1673, 1742, 1817, 1886, 1954, 2025, 2098, 2171, 2234, 2304, 2365, 2431]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[331, 557, 677, 777, 868, 960, 1050, 1136, 1223, 1307, 1390, 1466, 1536, 1603, 1673, 1741, 1814, 1889, 1954, 2028, 2096, 2164, 2233, 2305, 2362]}, {"subject_area"=>"/Biology and life sciences/Parasitology", "average_usage"=>[352, 609, 728, 831, 918, 998, 1091, 1195, 1289, 1369, 1442, 1504, 1573, 1647, 1722, 1799, 1877, 1938, 2013, 2106, 2166, 2242, 2306, 2371, 2452]}]}

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