miRNA Expression Profile Analysis in Kidney of Different Porcine Breeds
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{"title"=>"miRNA Expression Profile Analysis in Kidney of Different Porcine Breeds", "type"=>"journal", "authors"=>[{"first_name"=>"Oriol", "last_name"=>"Timoneda", "scopus_author_id"=>"55568796700"}, {"first_name"=>"Ingrid", "last_name"=>"Balcells", "scopus_author_id"=>"35739733000"}, {"first_name"=>"Jose Ignacio", "last_name"=>"Núñez", "scopus_author_id"=>"55568750500"}, {"first_name"=>"Raquel", "last_name"=>"Egea", "scopus_author_id"=>"24484579600"}, {"first_name"=>"Gonzalo", "last_name"=>"Vera", "scopus_author_id"=>"25222222500"}, {"first_name"=>"Anna", "last_name"=>"Castelló", "scopus_author_id"=>"7006870018"}, {"first_name"=>"Anna", "last_name"=>"Tomàs", "scopus_author_id"=>"24449610400"}, {"first_name"=>"Armand", "last_name"=>"Sánchez", "scopus_author_id"=>"7401886980"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0055402", "pui"=>"368187575", "sgr"=>"84872874130", "pmid"=>"23372853", "scopus"=>"2-s2.0-84872874130"}, "id"=>"b1326f8b-4284-3407-9cc0-a673224700aa", "abstract"=>"microRNAs (miRNAs) are important post-transcriptional regulators in eukaryotes that target mRNAs repressing their expression. The uncertain process of pig domestication, with different origin focuses, and the selection process that commercial breeds suffered, have generated a wide spectrum of breeds with clear genetic and phenotypic variability. The aim of this work was to define the miRNAs expression profile in kidney of several porcine breeds. Small RNA libraries from kidney were elaborated and high-throughput sequenced with the 454 Genome Sequencer FLX (Roche). Pigs used were classified into three groups: the European origin group (Iberian breed and European Wild Boar ancestor), European commercial breeds (Landrace, Large White and Piétrain breeds) and breeds with Asian origin (Meishan and Vietnamese breeds). A total of 229 miRNAs were described in the pig kidney miRNA profile, including 110 miRNAs out of the 257 previously described pig miRNAs and 119 orthologous miRNAs. The most expressed miRNAs in pig kidney microRNAome were Hsa-miR-200b-3p, Ssc-miR-125b and Ssc-miR-23b. Moreover, 5 novel porcine miRNAs and 3 orthologous miRNAs could be validated through RT-qPCR. miRNA sequence variation was determined in 116 miRNAs, evidencing the presence of isomiRs. 125 miRNAs were differentially expressed between breed groups. The identification of breed-specific miRNAs, which could be potentially associated to certain phenotypes, is becoming a new tool for the study of the genetic variability underlying complex traits and furthermore, it adds a new layer of complexity to the interesting process of pig evolution.", "link"=>"http://www.mendeley.com/research/mirna-expression-profile-analysis-kidney-different-porcine-breeds", "reader_count"=>19, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>7, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>7, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>2, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/500314"], "description"=>"<p><sup>1</sup>: <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055402#pone.0055402-Zuker1\" target=\"_blank\">[54]</a>. Orange line points out the miRNA position into the pre-miRNA structure.</p>", "links"=>[], "tags"=>["mirna", "folding", "candidates", "mirnas", "mfold"], "article_id"=>170829, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.g002", "stats"=>{"downloads"=>0, "page_views"=>55, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_miRNA_folding_for_cluster_candidates_to_novel_miRNAs_using_MFold_software_1_/170829", "title"=>"Predicted miRNA folding for cluster candidates to novel miRNAs using MFold software<sup>1</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-25 00:13:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/500535"], "description"=>"1<p>: miRBase (v18) homology (e-value≤1e-03). Internal mismatches were accepted.</p>2<p>: EU: European breeds. <sup>3</sup>: EA: European commercial breeds. <sup>4</sup>: AS: Asian breeds.</p><p>For HTS data, fold changes from sequence counting between breed groups were calculated from normalised data in counts per thousand for each library and averaged per groups. Positive and negative signs indicate that the level of gene expression is higher for the first or the second group of the test, respectively. Analysis of variance (ANOVA) including breed as fixed factor was performed. Significance was set at P<0.05. Fold changes for clusters could not be calculated due to their low total counts.</p><p>For qPCR data expression study, the quantity obtained of each miRNA in each sample was normalised by the Normalization Factor and corrected in relation to the lowest normalised value. Analysis of variance (ANOVA) including the RT and breed as fixed factors was performed and fold change from Least Squares Means (LSM) between breed groups were calculated. Significance was set at P<0.05. Scheffe test determined whether there was significant differential expression between breed groups (<sup>§</sup>: suggestive <i>p-value</i><0.1, <sup>*</sup>: significant with <i>p-value</i><0.05, <sup>**</sup>: significant with <i>p-value</i><0.01, <sup>***</sup>: significant with <i>p-value</i><0.001).</p>", "links"=>[], "tags"=>["hts", "differential", "rt-qpcr"], "article_id"=>171049, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.t006", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fold_Change_FC_comparison_from_HTS_differential_expression_study_and_RT_qPCR_data_/171049", "title"=>"Fold Change (FC) comparison from HTS differential expression study and RT-qPCR data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:17:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/500502"], "description"=>"1<p>: miRBase (v18) homology (e-value ≤1e-03). Internal mismatches were accepted.</p><p>Bta: <i>Bos taurus</i>, Hsa: <i>Homo sapiens</i>, <i>Ssc: Sus scrofa</i>.</p>", "links"=>[], "tags"=>["mirna", "putative", "mirnas", "further", "validation"], "article_id"=>171015, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.t005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_miRNA_and_putative_novel_miRNAs_Clusters_for_further_validation_through_RT_qPCR_/171015", "title"=>"Selected miRNA and putative novel miRNAs (Clusters) for further validation through RT-qPCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:16:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/500467"], "description"=>"1<p>: miRBase database (v18, November 2011).</p><p>Bta: <i>Bos taurus</i>, Hsa: <i>Homo sapiens</i>, Ssc: <i>Sus scrofa</i>.</p><p>Marked in bold the nucleotide variation between pair sequences.</p>", "links"=>[], "tags"=>["mirnas", "diverging", "mirna"], "article_id"=>170983, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.t004", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Most_expressed_miRNAs_diverging_between_the_reference_miRNA_sequence_and_the_miRBase_1_described_miRNA_sequence_/170983", "title"=>"Most expressed miRNAs diverging between the reference miRNA sequence and the miRBase<sup>1</sup> described miRNA sequence.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:16:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/500569"], "description"=>"<p>Primers used for the RT-qPCR validation design.</p>", "links"=>[], "tags"=>["rt-qpcr", "validation"], "article_id"=>171086, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_for_the_RT_qPCR_validation_design_/171086", "title"=>"Primers used for the RT-qPCR validation design.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:18:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/478898", "https://ndownloader.figshare.com/files/478899", "https://ndownloader.figshare.com/files/478900", "https://ndownloader.figshare.com/files/478901", "https://ndownloader.figshare.com/files/478902", "https://ndownloader.figshare.com/files/478903", "https://ndownloader.figshare.com/files/478904", "https://ndownloader.figshare.com/files/478905"], "description"=>"<div><p>microRNAs (miRNAs) are important post-transcriptional regulators in eukaryotes that target mRNAs repressing their expression. The uncertain process of pig domestication, with different origin focuses, and the selection process that commercial breeds suffered, have generated a wide spectrum of breeds with clear genetic and phenotypic variability. The aim of this work was to define the miRNAs expression profile in kidney of several porcine breeds. Small RNA libraries from kidney were elaborated and high-throughput sequenced with the 454 Genome Sequencer FLX (Roche). Pigs used were classified into three groups: the European origin group (Iberian breed and European Wild Boar ancestor), European commercial breeds (Landrace, Large White and Piétrain breeds) and breeds with Asian origin (Meishan and Vietnamese breeds). A total of 229 miRNAs were described in the pig kidney miRNA profile, including 110 miRNAs out of the 257 previously described pig miRNAs and 119 orthologous miRNAs. The most expressed miRNAs in pig kidney microRNAome were Hsa-miR-200b-3p, Ssc-miR-125b and Ssc-miR-23b. Moreover, 5 novel porcine miRNAs and 3 orthologous miRNAs could be validated through RT-qPCR. miRNA sequence variation was determined in 116 miRNAs, evidencing the presence of isomiRs. 125 miRNAs were differentially expressed between breed groups. The identification of breed-specific miRNAs, which could be potentially associated to certain phenotypes, is becoming a new tool for the study of the genetic variability underlying complex traits and furthermore, it adds a new layer of complexity to the interesting process of pig evolution.</p> </div>", "links"=>[], "tags"=>["mirna", "kidney", "porcine", "breeds"], "article_id"=>154410, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0055402.s001", "https://dx.doi.org/10.1371/journal.pone.0055402.s002", "https://dx.doi.org/10.1371/journal.pone.0055402.s003", "https://dx.doi.org/10.1371/journal.pone.0055402.s004", "https://dx.doi.org/10.1371/journal.pone.0055402.s005", "https://dx.doi.org/10.1371/journal.pone.0055402.s006", "https://dx.doi.org/10.1371/journal.pone.0055402.s007", "https://dx.doi.org/10.1371/journal.pone.0055402.s008"], "stats"=>{"downloads"=>23, "page_views"=>47, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/miRNA_Expression_Profile_Analysis_in_Kidney_of_Different_Porcine_Breeds__/154410", "title"=>"miRNA Expression Profile Analysis in Kidney of Different Porcine Breeds", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-25 01:13:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/500183"], "description"=>"<p>The number of total counts for each sequence is indicated. First sequence belongs to the precursor miRNA. Red bases match with precursor miRNA and belong to mature miRNA. Blue bases match also with precursor miRNA but do not belong to mature miRNA sequence. Sequence corresponding to the annotated miRNA in miRBase database is marked with an asterisk.</p>", "links"=>[], "tags"=>["variability"], "article_id"=>170692, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_variability_in_Ssc_miR_23b_/170692", "title"=>"Sequence variability in Ssc-miR-23b.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-25 00:11:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/500600"], "description"=>"1<p>: miRBase database (v18, November 2011).</p>*<p>Mismatches or gaps have not been allowed into the sequence alignment. Up to 4 mismatches allowed in the ends of the sequences.</p>", "links"=>[], "tags"=>["alignment", "mirbase"], "article_id"=>171117, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_sequence_alignment_with_miRBase_database_1_/171117", "title"=>"Summary of sequence alignment with miRBase database<sup>1</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:18:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/500632"], "description"=>"<p>IB: Iberian breed, WB: European Wild Boar, LD: Landrace breed, LW: Large White breed, PT: Piétrain breed, ME: Meishan breed, VT: Vietnamese breed.</p><p>miRNA name represents the most expressed miRNA sequence in the cluster.</p><p>Underlined miRNAs correspond to miRNAs that had not been previously described.</p><p>φ: miRNA clusters whose predominant isomiR is different from that described in miRBase database (v18, November 2011).</p>", "links"=>[], "tags"=>["abundant", "mirna", "kidney"], "article_id"=>171149, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Oriol Timoneda", "Ingrid Balcells", "Jose Ignacio Núñez", "Raquel Egea", "Gonzalo Vera", "Anna Castelló", "Anna Tomàs", "Armand Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055402.t003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Most_abundant_miRNA_profile_in_pig_kidney_CN_gt_350_/171149", "title"=>"Most abundant miRNA profile in pig kidney (CN>350).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:19:09"}

PMC Usage Stats | Further Information

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Relative Metric

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