Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish
Publication Date
January 08, 2013
Journal
PLOS ONE
Authors
Arjan P. Palstra, Sergi Beltran, Erik Burgerhout, Sebastiaan A. Brittijn, et al
Volume
8
Issue
1
Pages
e53171
DOI
https://dx.plos.org/10.1371/journal.pone.0053171
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0053171
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23308156
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540090
Europe PMC
http://europepmc.org/abstract/MED/23308156
Web of Science
000313429800031
Scopus
84872184626
Mendeley
http://www.mendeley.com/research/deep-rna-sequencing-skeletal-muscle-transcriptome-swimming-fish
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/512412"], "description"=>"<p>A) red muscle and B) white muscle. The green and red lines indicate thresholds of differential expression at RPKM = 0.5 and RPKM = 2, respectively. Larger, more abundant contigs show less noise in differential expression as determined by RPKM.</p>", "links"=>[], "tags"=>["plots", "reads", "kilobase", "mapped", "contigs", "grouped"], "article_id"=>182885, "categories"=>["Physiology", "Genetics"], "users"=>["Arjan P. Palstra", "Sergi Beltran", "Erik Burgerhout", "Sebastiaan A. Brittijn", "Leonardo J. Magnoni", "Christiaan V. Henkel", "Hans J. Jansen", "Guido E. E. J. M. van den Thillart", "Herman P. Spaink", "Josep V. Planas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053171.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MA_plots_of_the_ratio_vs_average_expression_by_Reads_Per_Kilobase_exon_model_per_Million_mapped_reads_RPKM_value_of_the_contigs_as_grouped_in_various_size_classes_/182885", "title"=>"MA plots of the ratio vs. average expression by Reads Per Kilobase (exon model) per Million mapped reads (RPKM) value of the contigs as grouped in various size classes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:48:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/512579"], "description"=>"<p>The red muscle transcriptome (red bars) was tested against the white muscle transcriptome (blue bars). Significant differences by a corrected p-value for multiple testing False Discovery Rate (FDR) are indicated by ** FDR≤0.01 and * FDR≤0.05. Significant differential expression was found for biological processes including twitch skeletal muscle contraction, voluntary skeletal muscle contraction and skeletal muscle contraction; for molecular functions including nucleoside-triphosphatase regulator activity, GTPase regulator activity and cytoskeletal protein binding; and cellular components including sarcomere, contractile fiber part, axoneme, sarcoplasmic reticulum membrane and myosin complex. In all cases, the percentage of sequences was higher in red than in white muscle.</p>", "links"=>[], "tags"=>["genetics and genomics", "physiology"], "article_id"=>183063, "categories"=>["Physiology", "Genetics"], "users"=>["Arjan P. Palstra", "Sergi Beltran", "Erik Burgerhout", "Sebastiaan A. Brittijn", "Leonardo J. Magnoni", "Christiaan V. Henkel", "Hans J. Jansen", "Guido E. E. J. M. van den Thillart", "Herman P. Spaink", "Josep V. Planas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053171.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_GO_term_distribution_between_red_and_white_muscle_/183063", "title"=>"Differential GO term distribution between red and white muscle.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:51:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/512754"], "description"=>"<p>Illustrated as pie charts are the six largest categories in red muscle (A) and white muscle (B) at biological process level 2 with the numbers of sequences per category indicated. Gene ontology processes are cellular process; metabolic process; localization; biological regulation; multicellular organismal process and developmental process in both red and white muscle without any relevant percentual differences between both tissues. Categories are however represented by a larger number of sequences in red muscle than in white muscle.</p>", "links"=>[], "tags"=>["ontology", "contigs"], "article_id"=>183240, "categories"=>["Physiology", "Genetics"], "users"=>["Arjan P. Palstra", "Sergi Beltran", "Erik Burgerhout", "Sebastiaan A. Brittijn", "Leonardo J. Magnoni", "Christiaan V. Henkel", "Hans J. Jansen", "Guido E. E. J. M. van den Thillart", "Herman P. Spaink", "Josep V. Planas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053171.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_of_the_large_contigs_8805_500_nt_in_red_and_white_muscle_/183240", "title"=>"Gene ontology of the large contigs (≥500 nt) in red and white muscle.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:54:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/512881"], "description"=>"<p>Selection of novel rainbow trout genes grouped by functional categories.</p>", "links"=>[], "tags"=>["rainbow", "trout", "genes", "grouped"], "article_id"=>183365, "categories"=>["Physiology", "Genetics"], "users"=>["Arjan P. Palstra", "Sergi Beltran", "Erik Burgerhout", "Sebastiaan A. Brittijn", "Leonardo J. Magnoni", "Christiaan V. Henkel", "Hans J. Jansen", "Guido E. E. J. M. van den Thillart", "Herman P. Spaink", "Josep V. Planas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053171.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selection_of_novel_rainbow_trout_genes_grouped_by_functional_categories_/183365", "title"=>"Selection of novel rainbow trout genes grouped by functional categories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-08 00:56:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/512922"], "description"=>"<p>Numbers and maximum size of assembled contigs, differential contig expression by Reads Per Kilobase (exon model) per Million mapped reads (RPKM) values, iterative BLAST annotation results and differentially expressed contigs ≥500 nt are indicated.</p>", "links"=>[], "tags"=>["annotation"], "article_id"=>183409, "categories"=>["Physiology", "Genetics"], "users"=>["Arjan P. Palstra", "Sergi Beltran", "Erik Burgerhout", "Sebastiaan A. Brittijn", "Leonardo J. Magnoni", "Christiaan V. Henkel", "Hans J. Jansen", "Guido E. E. J. M. van den Thillart", "Herman P. Spaink", "Josep V. Planas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053171.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_from_de_novo_assembly_and_annotation_per_tissue_red_or_white_muscle_/183409", "title"=>"Results from <i>de novo</i> assembly and annotation per tissue (red or white muscle).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-08 00:56:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/512959"], "description"=>"<p>The number of 51 nucleotides (nt) sequence reads, mapped reads (unique or non-unique) and unmapped reads for each individual group (red muscle or white muscle of resters or swimmers) are indicated.</p>", "links"=>[], "tags"=>["illumina"], "article_id"=>183448, "categories"=>["Physiology", "Genetics"], "users"=>["Arjan P. Palstra", "Sergi Beltran", "Erik Burgerhout", "Sebastiaan A. Brittijn", "Leonardo J. Magnoni", "Christiaan V. Henkel", "Hans J. Jansen", "Guido E. E. J. M. van den Thillart", "Herman P. Spaink", "Josep V. Planas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053171.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_of_Illumina_sequencing_/183448", "title"=>"Summary statistics of Illumina sequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-08 00:57:28"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
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Relative Metric

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