CiteULike | Further Information

• {"link"=>{"url"=>"http://www.citeulike.org/user/golharam/article/8500917"}, "post_time"=>"2011-01-03 20:12:38", "tag"=>["rna-seq", "t_brucei"], "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.ppat.1001090"}, "username"=>"golharam", "article_id"=>"8500917"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/kapila/article/11526612"}, "post_time"=>"2012-10-22 19:54:13", "tag"=>"no-tag", "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.ppat.1001090"}, "username"=>"kapila", "article_id"=>"11526612"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/mandr/article/11913562"}, "post_time"=>"2013-01-18 11:43:56", "tag"=>"trypanosoma", "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.ppat.1001090"}, "username"=>"mandr", "article_id"=>"11913562"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/jonathanjacobs/article/13552546"}, "post_time"=>"2015-03-17 19:19:24", "tag"=>"no-tag", "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.ppat.1001090"}, "username"=>"jonathanjacobs", "article_id"=>"13552546"}

Mendeley | Further Information

{"title"=>"The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution", "type"=>"journal", "authors"=>[{"first_name"=>"Nikolay G.", "last_name"=>"Kolev", "scopus_author_id"=>"9134082600"}, {"first_name"=>"Joseph B.", "last_name"=>"Franklin", "scopus_author_id"=>"56266384800"}, {"first_name"=>"Shai", "last_name"=>"Carmi", "scopus_author_id"=>"12784621900"}, {"first_name"=>"Huafang", "last_name"=>"Shi", "scopus_author_id"=>"7402622763"}, {"first_name"=>"Shulamit", "last_name"=>"Michaeli", "scopus_author_id"=>"7004557877"}, {"first_name"=>"Christian", "last_name"=>"Tschudi", "scopus_author_id"=>"7006405999"}], "year"=>2010, "source"=>"PLoS Pathogens", "identifiers"=>{"issn"=>"15537366", "scopus"=>"2-s2.0-78149292214", "pui"=>"359909828", "doi"=>"10.1371/journal.ppat.1001090", "isbn"=>"1553-7374 (Electronic)\\n1553-7366 (Linking)", "sgr"=>"78149292214", "pmid"=>"20838601"}, "id"=>"573d23d6-d325-3afd-9081-a541f18bd544", "abstract"=>"The genome of Trypanosoma brucei, the causative agent of African trypanosomiasis, was published five years ago, yet identification of all genes and their transcripts remains to be accomplished. Annotation is challenged by the organization of genes transcribed by RNA polymerase II (Pol II) into long unidirectional gene clusters with no knowledge of how transcription is initiated. Here we report a single-nucleotide resolution genomic map of the T. brucei transcriptome, adding 1,114 new transcripts, including 103 non-coding RNAs, confirming and correcting many of the annotated features and revealing an extensive heterogeneity of 5' and 3' ends. Some of the new transcripts encode polypeptides that are either conserved in T. cruzi and Leishmania major or were previously detected in mass spectrometry analyses. High-throughput RNA sequencing (RNA-Seq) was sensitive enough to detect transcripts at putative Pol II transcription initiation sites. Our results, as well as recent data from the literature, indicate that transcription initiation is not solely restricted to regions at the beginning of gene clusters, but may occur at internal sites. We also provide evidence that transcription at all putative initiation sites in T. brucei is bidirectional, a recently recognized fundamental property of eukaryotic promoters. Our results have implications for gene expression patterns in other important human pathogens with similar genome organization (Trypanosoma cruzi, Leishmania sp.) and revealed heterogeneity in pre-mRNA processing that could potentially contribute to the survival and success of the parasite population in the insect vector and the mammalian host.", "link"=>"http://www.mendeley.com/research/transcriptome-human-pathogen-trypanosoma-brucei-singlenucleotide-resolution", "reader_count"=>199, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>16, "Researcher"=>38, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>66, "Student > Postgraduate"=>11, "Other"=>4, "Student > Master"=>21, "Student > Bachelor"=>16, "Lecturer"=>2, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>16, "Researcher"=>38, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>66, "Student > Postgraduate"=>11, "Other"=>4, "Student > Master"=>21, "Student > Bachelor"=>16, "Lecturer"=>2, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>32, "Agricultural and Biological Sciences"=>142, "Medicine and Dentistry"=>6, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Social Sciences"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>142}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>32}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "Sweden"=>1, "Belgium"=>1, "United States"=>3, "Uruguay"=>1, "Brazil"=>2, "United Kingdom"=>6, "Chile"=>1, "France"=>1, "Switzerland"=>1, "Germany"=>2, "Spain"=>1}, "group_count"=>7}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/414017", "https://ndownloader.figshare.com/files/414060", "https://ndownloader.figshare.com/files/414077", "https://ndownloader.figshare.com/files/414095", "https://ndownloader.figshare.com/files/414120", "https://ndownloader.figshare.com/files/414149", "https://ndownloader.figshare.com/files/414190", "https://ndownloader.figshare.com/files/414214", "https://ndownloader.figshare.com/files/414234", "https://ndownloader.figshare.com/files/414249", "https://ndownloader.figshare.com/files/414263", "https://ndownloader.figshare.com/files/414275", "https://ndownloader.figshare.com/files/414285", "https://ndownloader.figshare.com/files/414299", "https://ndownloader.figshare.com/files/414308", "https://ndownloader.figshare.com/files/414324", "https://ndownloader.figshare.com/files/414370", "https://ndownloader.figshare.com/files/414376", "https://ndownloader.figshare.com/files/414382", "https://ndownloader.figshare.com/files/414387", "https://ndownloader.figshare.com/files/414397", "https://ndownloader.figshare.com/files/414412", "https://ndownloader.figshare.com/files/414422", "https://ndownloader.figshare.com/files/414437", "https://ndownloader.figshare.com/files/414451", "https://ndownloader.figshare.com/files/414463", "https://ndownloader.figshare.com/files/414473", "https://ndownloader.figshare.com/files/414487", "https://ndownloader.figshare.com/files/414500", "https://ndownloader.figshare.com/files/414516"], "description"=>"<div><p>The genome of <em>Trypanosoma brucei</em>, the causative agent of African trypanosomiasis, was published five years ago, yet identification of all genes and their transcripts remains to be accomplished. Annotation is challenged by the organization of genes transcribed by RNA polymerase II (Pol II) into long unidirectional gene clusters with no knowledge of how transcription is initiated. Here we report a single-nucleotide resolution genomic map of the <em>T. brucei</em> transcriptome, adding 1,114 new transcripts, including 103 non-coding RNAs, confirming and correcting many of the annotated features and revealing an extensive heterogeneity of 5′ and 3′ ends. Some of the new transcripts encode polypeptides that are either conserved in <em>T. cruzi</em> and <em>Leishmania major</em> or were previously detected in mass spectrometry analyses. High-throughput RNA sequencing (RNA-Seq) was sensitive enough to detect transcripts at putative Pol II transcription initiation sites. Our results, as well as recent data from the literature, indicate that transcription initiation is not solely restricted to regions at the beginning of gene clusters, but may occur at internal sites. We also provide evidence that transcription at all putative initiation sites in <em>T. brucei</em> is bidirectional, a recently recognized fundamental property of eukaryotic promoters. Our results have implications for gene expression patterns in other important human pathogens with similar genome organization (<em>Trypanosoma cruzi</em>, <em>Leishmania</em> sp.) and revealed heterogeneity in pre-mRNA processing that could potentially contribute to the survival and success of the parasite population in the insect vector and the mammalian host.</p></div>", "links"=>[], "tags"=>["transcriptome", "pathogen", "single-nucleotide"], "article_id"=>141773, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.s001", "https://dx.doi.org/10.1371/journal.ppat.1001090.s002", "https://dx.doi.org/10.1371/journal.ppat.1001090.s003", "https://dx.doi.org/10.1371/journal.ppat.1001090.s004", "https://dx.doi.org/10.1371/journal.ppat.1001090.s005", "https://dx.doi.org/10.1371/journal.ppat.1001090.s006", "https://dx.doi.org/10.1371/journal.ppat.1001090.s007", "https://dx.doi.org/10.1371/journal.ppat.1001090.s008", "https://dx.doi.org/10.1371/journal.ppat.1001090.s009", "https://dx.doi.org/10.1371/journal.ppat.1001090.s010", "https://dx.doi.org/10.1371/journal.ppat.1001090.s011", "https://dx.doi.org/10.1371/journal.ppat.1001090.s012", "https://dx.doi.org/10.1371/journal.ppat.1001090.s013", "https://dx.doi.org/10.1371/journal.ppat.1001090.s014", "https://dx.doi.org/10.1371/journal.ppat.1001090.s015", "https://dx.doi.org/10.1371/journal.ppat.1001090.s016", "https://dx.doi.org/10.1371/journal.ppat.1001090.s017", "https://dx.doi.org/10.1371/journal.ppat.1001090.s018", "https://dx.doi.org/10.1371/journal.ppat.1001090.s019", "https://dx.doi.org/10.1371/journal.ppat.1001090.s020", "https://dx.doi.org/10.1371/journal.ppat.1001090.s021", "https://dx.doi.org/10.1371/journal.ppat.1001090.s022", "https://dx.doi.org/10.1371/journal.ppat.1001090.s023", "https://dx.doi.org/10.1371/journal.ppat.1001090.s024", "https://dx.doi.org/10.1371/journal.ppat.1001090.s025", "https://dx.doi.org/10.1371/journal.ppat.1001090.s026", "https://dx.doi.org/10.1371/journal.ppat.1001090.s027", "https://dx.doi.org/10.1371/journal.ppat.1001090.s028", "https://dx.doi.org/10.1371/journal.ppat.1001090.s029", "https://dx.doi.org/10.1371/journal.ppat.1001090.s030"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Transcriptome_of_the_Human_Pathogen_Trypanosoma_brucei_at_Single_Nucleotide_Resolution/141773", "title"=>"The Transcriptome of the Human Pathogen <em>Trypanosoma brucei</em> at Single-Nucleotide Resolution", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-09-09 00:29:33"}
• {"files"=>["https://ndownloader.figshare.com/files/831335"], "description"=>"<p>(A) Outline of the protocol for generating libraries for sequencing. (B) Overlay of the number of reads (log₂) from 5′-end- (blue) and 3′-end- (red) enriched libraries aligning to ∼10 kb genomic region. Numbers of end-reads, SL-containing (blue) and poly(A)-containing (red), are shown below the x-axis (−log₂). (C–F) Examples of misannotated start codons (C), genes not producing their own transcript (D), alternatively processed transcripts (E) and new transcripts (F). Red arrows point to the highlighted transcriptome features.</p>", "links"=>[], "tags"=>["maps", "ends"], "article_id"=>501703, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RNA_Seq_precisely_maps_the_ends_of_T_brucei_transcripts_/501703", "title"=>"RNA-Seq precisely maps the ends of <i>T. brucei</i> transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:28:23"}
• {"files"=>["https://ndownloader.figshare.com/files/831490"], "description"=>"<p>(A) Distribution of 5′UTR length (including the 39 nt SL), n = 6,577. (B) Distribution of 3′UTR length, n = 1,902. (C–D) Coding potential of novel <i>T. brucei</i> transcripts. (C) Length distribution of possible ORF-encoded polypeptides (nonoverlapping ORFs, equal or longer than 75 nt), n = 4,540. (D) Positional distribution of translation start sites for possible ORFs in novel transcripts, n = 4,540.</p>", "links"=>[], "tags"=>["untranslated", "regions", "transcripts"], "article_id"=>501854, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_untranslated_regions_and_novel_transcripts_in_T_brucei_/501854", "title"=>"Characteristics of untranslated regions and novel transcripts in <i>T. brucei</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:30:54"}
• {"files"=>["https://ndownloader.figshare.com/files/831626"], "description"=>"<p>(A) Heterogeneity of 3′-<i>trans</i>-splice sites. The <i>trans</i>-splice sites of each gene are shown in each line of the plot, n = 7,966. Each site is represented by a bar colored according to its usage (relative number of SL-containing reads). The site with the largest number of reads is centered, and sites within 150 nt upstream or downstream of this site are included. For display purposes, not all transcripts are shown. Genes are ranked from most homogeneous splice sites (top) to least homogeneous splice sites (bottom). (B) Number of <i>trans</i>-splice sites per gene, n = 8,815. (C) Compositional profile of the 3′-<i>trans</i>-splice site sequence, n = 7,966. Nucleotide positions are relative to the site of splicing. (D) Distribution of PPT–3′-<i>trans</i>-splice site distances, n = 7,996. (E) Distribution of PPT lengths, n = 7,966. (F) Distribution of poly(A) site–(downstream-)3′-<i>trans</i>-splice site distances, n = 1,759.</p>", "links"=>[], "tags"=>["sites"], "article_id"=>501995, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trans_splice_sites_in_T_brucei_/501995", "title"=>"<i>Trans</i>-splice sites in <i>T. brucei</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:33:15"}
• {"files"=>["https://ndownloader.figshare.com/files/831750"], "description"=>"<p>(A) The polyadenylation sites of each gene are shown in each line of the plot, n = 2,081. Each site is represented by a bar colored according to its usage [relative number of poly(A)-containing reads]. The site with the largest number of reads is centered, and only sites within 150 nt upstream or downstream of this site are included. For display purposes, not all transcripts are shown. Genes are ranked from most homogeneous polyadenylation sites (top) to least homogeneous polyadenylation sites (bottom). (B) Compositional profile of <i>T. brucei</i> polyadenylation sites, n = 2,081.</p>", "links"=>[], "tags"=>["polyadenylation"], "article_id"=>502119, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heterogeneity_of_polyadenylation_sites_/502119", "title"=>"Heterogeneity of polyadenylation sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:35:19"}
• {"files"=>["https://ndownloader.figshare.com/files/831849"], "description"=>"<p>(A) Plots of the number of reads (log₂) from poly(A)-enriched (red) libraries and SL-enriched (blue) libraries aligning to a region of divergent transcription. a, b – transcripts underrepresented in the SL-enriched libraries. (B) Plots of the number of reads aligning to a region adjacent to a putative centromeric region on chromosome IV. c – a novel transcript, d – transcript underrepresented in the SL-enriched libraries. (C) Plots of the number of reads aligning to a region adjacent to a tRNA gene (green triangle). e – transcript underrepresented in the SL-enriched libraries. (D) Northern blots of RNA after one round of oligo(dT) selection with probes against the indicated transcripts. RNA size marker is visualized with methylene blue staining of the membrane. Multiple sizes transcripts are present for b and c, as suggested by the reads alignment plots in (A) and (B). Asterisks indicate bands cross-hybridizing to rRNA for the d and e blots. (E) RT-PCR assay to determine the nature of the 5′ ends of transcripts. After incubation of total RNA with the indicated enzymes, the samples were treated with or without Terminator exonuclease prior to reverse transcription and PCR. –RT – control sample without reverse transcriptase; Ctrl – control sample treated without any 5′-end-modifying enzyme; RPP – RNA 5′ polyphosphatase; TAP – tobacco acid pyrophosphatase; PNK – T4 polynucleotide kinase; CIP – calf intestinal alkaline phosphatase. Tb570 is a control detecting mRNA for Tb10.6k15.1610.</p>", "links"=>[], "tags"=>["transcripts", "sl", "suspected", "pol", "ii"], "article_id"=>502213, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Polyadenylated_transcripts_without_the_SL_sequence_at_suspected_Pol_II_start_sites_/502213", "title"=>"Polyadenylated transcripts without the SL sequence at suspected Pol II start sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:36:53"}
• {"files"=>["https://ndownloader.figshare.com/files/831949"], "description"=>"<p>(A) Shown is a segment of chromosome X surrounding the EP1 procyclin gene. The EP1 ORF is indicated by a dark blue arrow. The fold enrichment of reads from the 5′-triphosphate end library [(number of reads in the 5′-triphosphate end-enriched library)×24/(number of reads in the 5′-end enriched library)] are plotted for the plus strand (sense, red) and the minus strand (antisense, blue). (B) Shown is the region surrounding the transcription start site for RNA polymerase I with the individual aligned reads (blue horizontal arrows). Since this library was prepared after oligo(dT) selection of transcripts, the obtained reads are most likely derived from the extremely low-abundance, full-length polyadenylated EP1 procyclin transcripts that have not been <i>trans</i>-spliced. Indicated by arrows in different shades of orange-red are previously determined transcription start sites by S1 protection <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001090#ppat.1001090-Brown1\" target=\"_blank\">[52]</a> and primer extension <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001090#ppat.1001090-Pays1\" target=\"_blank\">[53]</a>, as well as the primary start site identified by RNA-Seq (this study).</p>", "links"=>[], "tags"=>["enriched", "ends", "captures", "transcription"], "article_id"=>502314, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_library_enriched_for_5_triphosphate_ends_accurately_captures_bona_fide_transcription_start_sites_/502314", "title"=>"A library enriched for 5′-triphosphate ends accurately captures <i>bona fide</i> transcription start sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:38:34"}
• {"files"=>["https://ndownloader.figshare.com/files/832020"], "description"=>"<p>Plots for the fold enrichment of reads from the 5′-triphosphate end library [(number of reads in the 5′-triphosphate end-enriched library)×24/(number of reads in the 5′-end enriched library)] are shown aligning to ∼40 kb genomic region for the plus strand (red) and the minus strand (blue). Annotated ORFs are shown in colored bars corresponding to their orientation. Annotated tRNAs are shown as green bars and are highlighted with green circles. (A) Plots for the examples shown in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001090#ppat-1001090-g005\" target=\"_blank\">Figure 5A–C</a>. (B) Examples of regions of divergent transcription. (C) Examples of genomic loci in proximity to tRNA genes. (D) Examples of genomic regions within transcription units.</p>", "links"=>[], "tags"=>["pol", "ii", "initiation", "sites"], "article_id"=>502382, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Putative_Pol_II_initiation_sites_in_T_brucei_/502382", "title"=>"Putative Pol II initiation sites in <i>T. brucei</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:39:42"}
• {"files"=>["https://ndownloader.figshare.com/files/832195"], "description"=>"<p>(A) Examples of homogeneous (left) and heterogeneous (right) <i>trans</i>-splice sites. Shown is the pileup of number of internal reads (log₂) from 5′-end-enriched libraries (dark red). Individual SL-containing reads are depicted by red arrows under the graph. The identity of each gene is indicated above the black bar representing the beginning of the ORF. The light blue vertical lines are 100 nt apart. (B) Examples of homogeneous (left) and heterogeneous (right) polyadenylation sites. The pileup of number of internal reads (log₂) from 3′-end-enriched libraries (red) is depicted above the individual poly(A)-containing reads (red dots). Scale as in (<i>A</i>). (C) Examples of “truly” alternatively processed transcripts. The number of internal reads (log₂) from 5′-end- (dark red) and 3′-end-enriched (red) libraries aligning to the genomic regions surrounding the indicated ORFs (black arrows) are depicted. Easily identifiable peaks in the 3′-end-enriched libraries pileup (red arrows) and end-reads (not shown) indicate the alternative 3′ ends of the transcripts containing the ORFs. Note the scale difference from (A) and (B).</p>", "links"=>[], "tags"=>["pre-mrna", "patterns"], "article_id"=>502565, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Complexity_of_pre_mRNA_processing_patterns_in_T_brucei_/502565", "title"=>"Complexity of pre-mRNA processing patterns in <i>T. brucei</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-09 00:42:45"}
• {"files"=>["https://ndownloader.figshare.com/files/832302"], "description"=>"a<p>Pcs, pcr and pct indicate libraries from procyclic cells prepared with random primers, oligo(dT) primer and SL primer (for the second cDNA strand), respectively.</p>b<p>Length of reads did not allow extraction of end-reads.</p>", "links"=>[], "tags"=>["rna-seq"], "article_id"=>502669, "categories"=>["Genetics", "Medicine", "Molecular Biology"], "users"=>["Nikolay G. Kolev", "Joseph B. Franklin", "Shai Carmi", "Huafang Shi", "Shulamit Michaeli", "Christian Tschudi"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001090.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistics_for_RNA_Seq_data_sets_/502669", "title"=>"Statistics for RNA-Seq data sets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-09 00:44:29"}

PMC Usage Stats | Further Information

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F1000Prime | Further Information

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• {"year"=>2015, "month"=>1, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"http://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2015-01-26T09:40:37Z"}
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• {"year"=>2016, "month"=>7, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"http://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2016-07-25T08:40:34Z"}
• {"year"=>2016, "month"=>8, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"http://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2016-08-29T08:40:29Z"}
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• {"year"=>2016, "month"=>10, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"http://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2016-10-31T08:40:32Z"}
• {"year"=>2016, "month"=>11, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"http://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2016-11-28T09:40:33Z"}
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• {"year"=>2017, "month"=>1, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"http://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2017-01-30T09:40:34Z"}
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• {"year"=>2017, "month"=>4, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"http://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2017-04-24T08:40:24Z"}
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• {"year"=>2017, "month"=>8, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2017-08-28T08:40:46Z"}
• {"year"=>2017, "month"=>9, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2017-09-25T08:40:28Z"}
• {"year"=>2017, "month"=>10, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2017-10-30T08:40:44Z"}
• {"year"=>2017, "month"=>11, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2017-11-27T09:40:52Z"}
• {"year"=>2017, "month"=>12, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2017-12-25T09:40:40Z"}
• {"year"=>2018, "month"=>1, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2018-01-29T09:40:25Z"}
• {"year"=>2018, "month"=>2, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2018-02-26T09:40:26Z"}
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• {"year"=>2018, "month"=>8, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2018-08-27T08:40:34Z"}
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• {"year"=>2018, "month"=>12, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2018-12-31T09:40:45Z"}
• {"year"=>2019, "month"=>1, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-01-28T09:40:30Z"}
• {"year"=>2019, "month"=>2, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-02-25T09:40:33Z"}
• {"year"=>2019, "month"=>3, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-03-25T08:40:29Z"}
• {"year"=>2019, "month"=>4, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-04-29T08:40:32Z"}
• {"year"=>2019, "month"=>5, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-05-27T08:40:40Z"}
• {"year"=>2019, "month"=>6, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-06-24T08:40:33Z"}
• {"year"=>2019, "month"=>7, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-07-29T08:40:41Z"}
• {"year"=>2019, "month"=>8, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-08-26T08:40:36Z"}
• {"year"=>2019, "month"=>9, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-09-30T08:40:39Z"}
• {"year"=>2019, "month"=>10, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-10-28T08:40:35Z"}
• {"year"=>2019, "month"=>11, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-11-25T09:40:39Z"}
• {"year"=>2019, "month"=>12, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2019-12-30T09:40:36Z"}
• {"year"=>2020, "month"=>1, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-01-27T09:40:34Z"}
• {"year"=>2020, "month"=>2, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-02-24T09:40:39Z"}
• {"year"=>2020, "month"=>3, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-03-30T08:40:41Z"}
• {"year"=>2020, "month"=>4, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-04-27T08:40:35Z"}
• {"year"=>2020, "month"=>5, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-05-25T08:40:36Z"}
• {"year"=>2020, "month"=>6, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-06-29T08:40:35Z"}
• {"year"=>2020, "month"=>7, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-07-27T08:40:36Z"}
• {"year"=>2020, "month"=>8, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-08-31T08:40:37Z"}
• {"year"=>2020, "month"=>9, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-09-28T08:40:39Z"}
• {"year"=>2020, "month"=>10, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-10-26T08:40:36Z"}
• {"year"=>2020, "month"=>11, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-11-30T09:40:40Z"}
• {"year"=>2020, "month"=>12, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2020-12-28T09:40:38Z"}
• {"year"=>2021, "month"=>1, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2021-01-25T09:40:38Z"}
• {"year"=>2021, "month"=>2, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2021-02-22T09:40:36Z"}
• {"year"=>2021, "month"=>3, "doi"=>"10.1371/journal.ppat.1001090", "f1000_id"=>"6118956", "url"=>"https://f1000.com/prime/6118956", "score"=>1, "classifications"=>[], "updated_at"=>"2021-03-01T09:40:32Z"}