De Novo Characterization of Fall Dormant and Nondormant Alfalfa (Medicago sativa L.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy
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{"title"=>"De novo characterization of fall dormant and nondormant alfalfa (Medicago sativa L) leaf transcriptome and identification of candidate genes related to fall dormancy", "type"=>"journal", "authors"=>[{"first_name"=>"Senhao", "last_name"=>"Zhang", "scopus_author_id"=>"56058111600"}, {"first_name"=>"Yinghua", "last_name"=>"Shi", "scopus_author_id"=>"14070754500"}, {"first_name"=>"Ningning", "last_name"=>"Cheng", "scopus_author_id"=>"56573439600"}, {"first_name"=>"Hongqi", "last_name"=>"Du", "scopus_author_id"=>"56438562600"}, {"first_name"=>"Wenna", "last_name"=>"Fan", "scopus_author_id"=>"56438556200"}, {"first_name"=>"Chengzhang", "last_name"=>"Wang", "scopus_author_id"=>"55883658100"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "sgr"=>"84925762311", "scopus"=>"2-s2.0-84925762311", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "pui"=>"603282202", "doi"=>"10.1371/journal.pone.0122170", "pmid"=>"25799491"}, "id"=>"f9467df8-1354-3288-b39f-ac20c36f5a18", "abstract"=>"Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. The physiological, biochemical and molecular mechanisms causing fall dormancy and the related genes have not been well studied. In this study, we sequenced two standard varieties of alfalfa (dormant and non-dormant) at two time points and generated approximately 160 million high quality paired-end sequence reads using sequencing by synthesis (SBS) technology. The de novo transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa leaf transcriptome. After assembly, 111,062 (57.6%) transcripts were annotated against the NCBI non-redundant database. A total of 30,165 (15.6%) transcripts were mapped to 323 Kyoto Encyclopedia of Genes and Genomes pathways. We also identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa, and 1,541 transcription factors were identified across 1,350 transcripts. Gene expression between dormant and non-dormant alfalfa at different time points were performed, and we identified several differentially expressed genes potentially related to fall dormancy. The Gene Ontology and pathways information were also identified. We sequenced and assembled the leaf transcriptome of alfalfa related to fall dormancy, and also identified some genes of interest involved in the fall dormancy mechanism. Thus, our research focused on studying fall dormancy in alfalfa through transcriptome sequencing. The sequencing and gene expression data generated in this study may be used further to elucidate the complete mechanisms governing fall dormancy in alfalfa.", "link"=>"http://www.mendeley.com/research/novo-characterization-fall-dormant-nondormant-alfalfa-medicago-sativa-l-leaf-transcriptome-identific", "reader_count"=>11, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>3, "Student > Master"=>2}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>3, "Student > Master"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>7, "Medicine and Dentistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Greece"=>1, "Brazil"=>1, "Mexico"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1983156"], "description"=>"<p>Alfalfa leaf transcriptome was subjected to NCBI NR database for sequence similarity search using BLASTX (E-value threshold of ≤ 1E-05). Values above bars show the number of transcripts hit in each species.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351533, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_distribution_of_BLASTX_top_hits_against_NCBI_NR_database_/1351533", "title"=>"Species distribution of BLASTX top hits against NCBI NR database.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983173"], "description"=>"<p>Differential expressed genes detected through NGS sequencing in our study were validated using qPCR. Twenty-two DE genes were randomly selected for validation. The correlation between NGS sequencing and qPCR was shown.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351550, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g011", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_qPCR_validation_/1351550", "title"=>"qPCR validation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983170"], "description"=>"<p>Node size is proportional to the number of transcripts in each category and the significance levels are color coded ranging from 5E-02 to <5E-07 (white, no significant difference; yellow, <i>P</i> = 0.05; orange, <i>P</i> < 5E-07).</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351547, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g010", "stats"=>{"downloads"=>1, "page_views"=>99, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_enriched_Gene_Ontology_categories_of_DE_genes_in_D9_vs_ND9_set_using_BiNGO_/1351547", "title"=>"Significantly enriched Gene Ontology categories of DE genes in D9 vs. ND9 set using BiNGO.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983155"], "description"=>"<p>A, Frequency of GC content of alfalfa leaf transcripts. B, Distribution of GC content of transcripts for alfalfa (<i>Medicago sativa</i>; Ms), <i>Medicago truncatula</i> (Mt), <i>Glycine max</i> (Gm), <i>Lotus japonicus</i> (Lj) and <i>Arabidopsis thaliana</i> (At). The box shows the interquartile range. The circles are outliers of the GC content.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351532, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GC_content_analysis_of_alfalfa_leaf_transcripts_/1351532", "title"=>"GC content analysis of alfalfa leaf transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983152"], "description"=>"<p>Lenth of the 192,875 transcripts in the alfalfa leaf transcriptome were illustrated. The length ranges from 200 bp to more than or equal to 3,000 bp.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351529, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_length_distribution_of_alfalfa_leaf_transcriptome_/1351529", "title"=>"Sequence length distribution of alfalfa leaf transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983181"], "description"=>"<p>Enriched pathways in ND9-specific genes.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351558, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.t006", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enriched_pathways_in_ND9_specific_genes_/1351558", "title"=>"Enriched pathways in ND9-specific genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983178"], "description"=>"<p>Summary of <i>de novo</i> assembled alfalfa leaf transcriptome.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351555, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.t002", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_de_novo_assembled_alfalfa_leaf_transcriptome_/1351555", "title"=>"Summary of <i>de novo</i> assembled alfalfa leaf transcriptome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983177"], "description"=>"<p>Plant height was measured using Mean±SD (standard deviation).</p><p>Natural height of plants selected for sequencing.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351554, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.t001", "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Natural_height_of_plants_selected_for_sequencing_/1351554", "title"=>"Natural height of plants selected for sequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983158"], "description"=>"<p>GO Slim terms were assigned to 77,307 transcripts and categorized into three groups: biological process (58,412), molecular function (63,602) and cellular component (42,472).</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351535, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_GO_distribution_of_alfalfa_leaf_transcripts_at_level_2_/1351535", "title"=>"Gene Ontology (GO) distribution of alfalfa leaf transcripts at level 2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983159"], "description"=>"<p>Of transcripts annotated, 13,699 were classified into 25 KOG categories.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351536, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_EuKaryotic_Orthologous_Groups_KOG_classifications_of_alfalfa_transcripts_/1351536", "title"=>"EuKaryotic Orthologous Groups (KOG) classifications of alfalfa transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983187", "https://ndownloader.figshare.com/files/1983188", "https://ndownloader.figshare.com/files/1983189", "https://ndownloader.figshare.com/files/1983190", "https://ndownloader.figshare.com/files/1983191", "https://ndownloader.figshare.com/files/1983192", "https://ndownloader.figshare.com/files/1983193", "https://ndownloader.figshare.com/files/1983194", "https://ndownloader.figshare.com/files/1983195", "https://ndownloader.figshare.com/files/1983196", "https://ndownloader.figshare.com/files/1983197"], "description"=>"<div><p>Alfalfa (<i>Medicago sativa</i> L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. The physiological, biochemical and molecular mechanisms causing fall dormancy and the related genes have not been well studied. In this study, we sequenced two standard varieties of alfalfa (dormant and non-dormant) at two time points and generated approximately 160 million high quality paired-end sequence reads using sequencing by synthesis (SBS) technology. The <i>de novo</i> transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa leaf transcriptome. After assembly, 111,062 (57.6%) transcripts were annotated against the NCBI non-redundant database. A total of 30,165 (15.6%) transcripts were mapped to 323 Kyoto Encyclopedia of Genes and Genomes pathways. We also identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa, and 1,541 transcription factors were identified across 1,350 transcripts. Gene expression between dormant and non-dormant alfalfa at different time points were performed, and we identified several differentially expressed genes potentially related to fall dormancy. The Gene Ontology and pathways information were also identified. We sequenced and assembled the leaf transcriptome of alfalfa related to fall dormancy, and also identified some genes of interest involved in the fall dormancy mechanism. Thus, our research focused on studying fall dormancy in alfalfa through transcriptome sequencing. The sequencing and gene expression data generated in this study may be used further to elucidate the complete mechanisms governing fall dormancy in alfalfa.</p></div>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351564, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0122170.s001", "https://dx.doi.org/10.1371/journal.pone.0122170.s002", "https://dx.doi.org/10.1371/journal.pone.0122170.s003", "https://dx.doi.org/10.1371/journal.pone.0122170.s004", "https://dx.doi.org/10.1371/journal.pone.0122170.s005", "https://dx.doi.org/10.1371/journal.pone.0122170.s006", "https://dx.doi.org/10.1371/journal.pone.0122170.s007", "https://dx.doi.org/10.1371/journal.pone.0122170.s008", "https://dx.doi.org/10.1371/journal.pone.0122170.s009", "https://dx.doi.org/10.1371/journal.pone.0122170.s010", "https://dx.doi.org/10.1371/journal.pone.0122170.s011"], "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_De_Novo_Characterization_of_Fall_Dormant_and_Nondormant_Alfalfa_Medicago_sativa_L_Leaf_Transcriptome_and_Identification_of_Candidate_Genes_Related_to_Fall_Dormancy/1351564", "title"=>"<i>De Novo</i> Characterization of Fall Dormant and Nondormant Alfalfa (<i>Medicago sativa L</i>.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983153"], "description"=>"<p>It was performed using BLASTX with an E-value threshold of ≤ 1E-05.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351530, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similarity_of_alfalfa_leaf_transcriptome_with_proteomes_of_fifteen_sequenced_plants_/1351530", "title"=>"Similarity of alfalfa leaf transcriptome with proteomes of fifteen sequenced plants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983167"], "description"=>"<p>Node size is proportional to the number of transcripts in each category and the significance levels are color coded ranging from 5E-02 to < 5E-07 (white, no significant difference; yellow, <i>P</i> = 0.05; orange, <i>P</i> < 5E-07).</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351544, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g009", "stats"=>{"downloads"=>6, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_enriched_Gene_Ontology_categories_of_DE_genes_in_D5_vs_D9_set_using_BiNGO_/1351544", "title"=>"Significantly enriched Gene Ontology categories of DE genes in D5 vs. D9 set using BiNGO.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983180"], "description"=>"<p>Enriched KEGG pathways in D9-specific genes.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351557, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.t005", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enriched_KEGG_pathways_in_D9_specific_genes_/1351557", "title"=>"Enriched KEGG pathways in D9-specific genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983165"], "description"=>"<p>DE genes were filtered with at least 2-fold change and adjusted <i>P</i> value less than 0.01. Green and red box shows the quantity of annotated and un-annotated DE genes against NCBI NR database (using BLASTX with an E-value threshold of ≤ 1E-05). DE genes above the x-axis were up regulated ones, below were down regulated.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351542, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g008", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_differential_expressed_DE_genes_identified_in_our_study_/1351542", "title"=>"Number of differential expressed (DE) genes identified in our study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983162"], "description"=>"<p>Transcription factors were identified using BLASTX with an E-value threshold of ≤ 1E-05 against the PlnTFDB. A total of 1,541 transcription factors were identified in 81 transcription factor families.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351539, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g007", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcription_factor_families_identified_in_alfalfa_leaf_transcriptome_/1351539", "title"=>"Transcription factor families identified in alfalfa leaf transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983179"], "description"=>"<p>Statistics of SSRs identified in alfalfa leaf transcriptome.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351556, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.t004", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistics_of_SSRs_identified_in_alfalfa_leaf_transcriptome_/1351556", "title"=>"Statistics of SSRs identified in alfalfa leaf transcriptome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-23 05:50:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1983175"], "description"=>"<p>Of the total of 94,700 genes in transcriptome, 41,763 (44.10%) were shared by all of the four sets.D5, ND5, D9 and ND9 for dormant type (Maverick) in May, non-dormant type (CUF101) in May, dormant type in September and non-dormant type in September, respectively.</p>", "links"=>[], "tags"=>["gene expression data", "sequencing", "ncbi", "Candidate Genes Related", "time points", "sbs", "Fall Dormancy Alfalfa", "De Novo Characterization", "fall dormancy mechanism", "323 Kyoto Encyclopedia", "fall dormancy", "alfalfa leaf transcriptome"], "article_id"=>1351553, "categories"=>["Biological Sciences"], "users"=>["Senhao Zhang", "Yinghua Shi", "Ningning Cheng", "Hongqi Du", "Wenna Fan", "Chengzhang Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122170.g012", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Common_and_specific_genes_among_or_in_each_of_the_four_conditions_in_our_study_/1351553", "title"=>"Common and specific genes among or in each of the four conditions in our study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 05:50:50"}

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  • {"unique-ip"=>"18", "full-text"=>"12", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"9", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
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  • {"unique-ip"=>"11", "full-text"=>"14", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"11", "full-text"=>"14", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"7", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
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  • {"unique-ip"=>"16", "full-text"=>"18", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"12", "full-text"=>"19", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"16", "full-text"=>"11", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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