MicroRNAome of Porcine Pre- and Postnatal Development
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{"title"=>"MicroRNAome of porcine pre- and postnatal development", "type"=>"journal", "authors"=>[{"first_name"=>"Mingzhou", "last_name"=>"Li", "scopus_author_id"=>"24081034600"}, {"first_name"=>"Youlin", "last_name"=>"Xia", "scopus_author_id"=>"7403022398"}, {"first_name"=>"Yiren", "last_name"=>"Gu", "scopus_author_id"=>"24764432400"}, {"first_name"=>"Kai", "last_name"=>"Zhang", "scopus_author_id"=>"55249774900"}, {"first_name"=>"Qiulei", "last_name"=>"Lang", "scopus_author_id"=>"8930784400"}, {"first_name"=>"Lei", "last_name"=>"Chen", "scopus_author_id"=>"7409441990"}, {"first_name"=>"Jiuqiang", "last_name"=>"Guan", "scopus_author_id"=>"36607880600"}, {"first_name"=>"Zonggang", "last_name"=>"Luo", "scopus_author_id"=>"36608618900"}, {"first_name"=>"Haosi", "last_name"=>"Chen", "scopus_author_id"=>"36607824600"}, {"first_name"=>"Yang", "last_name"=>"Li", "scopus_author_id"=>"57192524089"}, {"first_name"=>"Qinghai", "last_name"=>"Li", "scopus_author_id"=>"36627429500"}, {"first_name"=>"Xiang", "last_name"=>"Li", "scopus_author_id"=>"57192491565"}, {"first_name"=>"An an", "last_name"=>"Jiang", "scopus_author_id"=>"15839289300"}, {"first_name"=>"Surong", "last_name"=>"Shuai", "scopus_author_id"=>"15843891400"}, {"first_name"=>"Jinyong", "last_name"=>"Wang", "scopus_author_id"=>"15823136900"}, {"first_name"=>"Qi", "last_name"=>"Zhu", "scopus_author_id"=>"36629559200"}, {"first_name"=>"Xiaochuan", "last_name"=>"Zhou", "scopus_author_id"=>"7410091234"}, {"first_name"=>"Xiaolian", "last_name"=>"Gao", "scopus_author_id"=>"7403873000"}, {"first_name"=>"Xuewei", "last_name"=>"Li", "scopus_author_id"=>"7501709448"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"77955388999", "doi"=>"10.1371/journal.pone.0011541", "pui"=>"359318739", "pmid"=>"20634961", "scopus"=>"2-s2.0-77955388999", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"a9cdf2ae-6e4c-39ce-b723-a4862baa1af5", "abstract"=>"The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies.", "link"=>"http://www.mendeley.com/research/micrornaome-porcine-pre-postnatal-development", "reader_count"=>63, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>6, "Student > Doctoral Student"=>5, "Researcher"=>15, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>6, "Student > Doctoral Student"=>5, "Researcher"=>15, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>45, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>45}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Belgium"=>1, "China"=>1, "Brazil"=>1, "Italy"=>1, "India"=>1}, "group_count"=>3}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/840994"], "description"=>"<p>(A) The length distribution of sequenced small RNAs. The red-pinkish colors indicate prenatal samples and blue colors indicate postnatal samples. (B) Plot of the unique miRNAs (starting from the miRNA with the highest counts, x-axis) versus their accumulative % in total counts of the mappable sequences. The dashed horizontal line at 54.3% represents the level of the total 771 unique miRNAs and the % of individual miRNA is marked by the gray line.</p>", "links"=>[], "tags"=>["counts", "characteristics", "sequencing"], "article_id"=>511420, "categories"=>["Medicine", "Genetics"], "users"=>["Mingzhou Li", "Youlin Xia", "Yiren Gu", "Kai Zhang", "Qiulei Lang", "Lei Chen", "Jiuqiang Guan", "Zonggang Luo", "Haosi Chen", "Yang Li", "Qinghai Li", "Xiang Li", "An-an Jiang", "Surong Shuai", "Jinyong Wang", "Qi Zhu", "Xiaochuan Zhou", "Xiaolian Gao", "Xuewei Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011541.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_length_and_counts_characteristics_of_the_sequencing_results_/511420", "title"=>"The length and counts characteristics of the sequencing results.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-12 00:23:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/841551"], "description"=>"<p>(A) The chromosomal locations of the porcine pre-miRNAs (mir, black lines) and 59 clusters (under the MID is limited to 50 kb, black dots) are displayed across 19 chromosomes. (B) The comparison of pre-miRNA densities (number of pre-miRNAs per Mb of chromosome) on the X chromosome (dark bar) and autosomes (gray bar) for pig and other seven well-studies mammals is shown pair-wise with the corresponding ratio given in parenthesis. The genome coordinates of pre-miRNAs were derived from miRBase 14.0.</p>", "links"=>[], "tags"=>["porcine"], "article_id"=>511998, "categories"=>["Medicine", "Genetics"], "users"=>["Mingzhou Li", "Youlin Xia", "Yiren Gu", "Kai Zhang", "Qiulei Lang", "Lei Chen", "Jiuqiang Guan", "Zonggang Luo", "Haosi Chen", "Yang Li", "Qinghai Li", "Xiang Li", "An-an Jiang", "Surong Shuai", "Jinyong Wang", "Qi Zhu", "Xiaochuan Zhou", "Xiaolian Gao", "Xuewei Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011541.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chromosomal_organization_of_the_porcine_pre_miRNAs_/511998", "title"=>"Chromosomal organization of the porcine pre-miRNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-12 00:33:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/419428", "https://ndownloader.figshare.com/files/419543", "https://ndownloader.figshare.com/files/419620", "https://ndownloader.figshare.com/files/419668", "https://ndownloader.figshare.com/files/419789", "https://ndownloader.figshare.com/files/419910", "https://ndownloader.figshare.com/files/420004", "https://ndownloader.figshare.com/files/420049", "https://ndownloader.figshare.com/files/420061", "https://ndownloader.figshare.com/files/420071", "https://ndownloader.figshare.com/files/420085", "https://ndownloader.figshare.com/files/420096", "https://ndownloader.figshare.com/files/420105", "https://ndownloader.figshare.com/files/420118", "https://ndownloader.figshare.com/files/420140", "https://ndownloader.figshare.com/files/420155", "https://ndownloader.figshare.com/files/420172", "https://ndownloader.figshare.com/files/420183", "https://ndownloader.figshare.com/files/420194", "https://ndownloader.figshare.com/files/420205", "https://ndownloader.figshare.com/files/420222", "https://ndownloader.figshare.com/files/420229", "https://ndownloader.figshare.com/files/420241", "https://ndownloader.figshare.com/files/420250", "https://ndownloader.figshare.com/files/420256", "https://ndownloader.figshare.com/files/420263", "https://ndownloader.figshare.com/files/420272"], "description"=>"<div><p>The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies.</p></div>", "links"=>[], "tags"=>["micrornaome", "porcine", "pre-", "postnatal"], "article_id"=>142828, "categories"=>["Medicine", "Genetics"], "users"=>["Mingzhou Li", "Youlin Xia", "Yiren Gu", "Kai Zhang", "Qiulei Lang", "Lei Chen", "Jiuqiang Guan", "Zonggang Luo", "Haosi Chen", "Yang Li", "Qinghai Li", "Xiang Li", "An-an Jiang", "Surong Shuai", "Jinyong Wang", "Qi Zhu", "Xiaochuan Zhou", "Xiaolian Gao", "Xuewei Li"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0011541.s001", "https://dx.doi.org/10.1371/journal.pone.0011541.s002", "https://dx.doi.org/10.1371/journal.pone.0011541.s003", "https://dx.doi.org/10.1371/journal.pone.0011541.s004", "https://dx.doi.org/10.1371/journal.pone.0011541.s005", "https://dx.doi.org/10.1371/journal.pone.0011541.s006", "https://dx.doi.org/10.1371/journal.pone.0011541.s007", "https://dx.doi.org/10.1371/journal.pone.0011541.s008", "https://dx.doi.org/10.1371/journal.pone.0011541.s009", "https://dx.doi.org/10.1371/journal.pone.0011541.s010", "https://dx.doi.org/10.1371/journal.pone.0011541.s011", "https://dx.doi.org/10.1371/journal.pone.0011541.s012", "https://dx.doi.org/10.1371/journal.pone.0011541.s013", "https://dx.doi.org/10.1371/journal.pone.0011541.s014", "https://dx.doi.org/10.1371/journal.pone.0011541.s015", "https://dx.doi.org/10.1371/journal.pone.0011541.s016", "https://dx.doi.org/10.1371/journal.pone.0011541.s017", "https://dx.doi.org/10.1371/journal.pone.0011541.s018", "https://dx.doi.org/10.1371/journal.pone.0011541.s019", "https://dx.doi.org/10.1371/journal.pone.0011541.s020", "https://dx.doi.org/10.1371/journal.pone.0011541.s021", "https://dx.doi.org/10.1371/journal.pone.0011541.s022", "https://dx.doi.org/10.1371/journal.pone.0011541.s023", "https://dx.doi.org/10.1371/journal.pone.0011541.s024", "https://dx.doi.org/10.1371/journal.pone.0011541.s025", "https://dx.doi.org/10.1371/journal.pone.0011541.s026", "https://dx.doi.org/10.1371/journal.pone.0011541.s027"], "stats"=>{"downloads"=>49, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/MicroRNAome_of_Porcine_Pre_and_Postnatal_Development/142828", "title"=>"MicroRNAome of Porcine Pre- and Postnatal Development", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-07-12 00:47:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/841339"], "description"=>"<p>(A) Plot of miRNAs detected in one (1-lib), two (2-lib), … 10-libraries (10-lib). The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in 1-lib, 73/144 means that 73 mammalian-conserved miRNAs and 144 pig-specific are present once in the 10 libraries. The bar graphs are depicted in a similar fashion. (B) Plot of miRNAs detected in each sample. The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in E30d, 168/18 means that 168 mammalian-conserved and 18 pig-specific miRNAs were detected in the E30d library. The bar graphs are depicted in a similar fashion. (C) The Venn diagram displays the distribution of 771 miRNAs through the pre- and postnatal stages (note that the classifications of the miRNAs may be overlapping due to assignment of miRNA to more than one kind of categories). Reading from left to right of the Figure shows the distribution of mammalian-conserved miRNAs, to be 42, 286, and 63 sequences (accounting 100%) for prenatal, co-expression, and postnatal stages, respectively; the distribution for pig-specific miRNAs is 111, 143, and 126 sequences (accounting 100%), respectively. The subclasses of the known, PN(a), PN(b) and PC are explained in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011541#pone.0011541.s012\" target=\"_blank\">Table S5</a>.</p>", "links"=>[], "tags"=>["kinds", "771", "mirnas", "libraries"], "article_id"=>511773, "categories"=>["Medicine", "Genetics"], "users"=>["Mingzhou Li", "Youlin Xia", "Yiren Gu", "Kai Zhang", "Qiulei Lang", "Lei Chen", "Jiuqiang Guan", "Zonggang Luo", "Haosi Chen", "Yang Li", "Qinghai Li", "Xiang Li", "An-an Jiang", "Surong Shuai", "Jinyong Wang", "Qi Zhu", "Xiaochuan Zhou", "Xiaolian Gao", "Xuewei Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011541.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expressed_kinds_of_771_unique_miRNAs_across_ten_libraries_are_summarized_/511773", "title"=>"Expressed kinds of 771 unique miRNAs across ten libraries are summarized.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-12 00:29:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/841153"], "description"=>"<p>(A) The total pre-miRNAs represented in miRBase (left) and an updated count by this study (right). The pre-miRNAs in four groups: type containing miR-5p (blue), miR-3p (tan), both miR-5p and miR-3p (brown), and miRNAs not detected in this study (white) in the pre-miRNAs. (B) The miRNAs from 16 pre-miRNAs which show patterns of both miR-5p and miR-3p or either miR-5p and miR-3p present in all ten libraries profiled over pre- and postnatal development stages. Data reflect the most abundant isomiRs scaled based on the total counts of the mappable sequences in each library shown in log<sub>2</sub>-scale. For each miRNA, “New” means miRNA identified in this study; “Diff” means our reported miRNA sequences are different from that of miRBase; “Yes” means our reported miRNA sequences are consistent with those of miRBase. The two miRNAs (miR-1a-3p and miR-122-5p) with the highest expression level (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011541#pone.0011541.s021\" target=\"_blank\">Table S14</a>) are marked by red dots.</p>", "links"=>[], "tags"=>["temporal", "porcine", "mirnas"], "article_id"=>511581, "categories"=>["Medicine", "Genetics"], "users"=>["Mingzhou Li", "Youlin Xia", "Yiren Gu", "Kai Zhang", "Qiulei Lang", "Lei Chen", "Jiuqiang Guan", "Zonggang Luo", "Haosi Chen", "Yang Li", "Qinghai Li", "Xiang Li", "An-an Jiang", "Surong Shuai", "Jinyong Wang", "Qi Zhu", "Xiaochuan Zhou", "Xiaolian Gao", "Xuewei Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011541.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_temporal_profile_of_the_known_porcine_miRNAs_and_new_miRNA_s_/511581", "title"=>"The temporal profile of the known porcine miRNAs and new miRNA*s.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-12 00:26:21"}

PMC Usage Stats | Further Information

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