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Annotation table - Whole body transcriptomes of the tick Ixodes ricinus at different stage and feeding conditions

N Pierre Charrier; Marjorie Couton; Maarten J Voordouw; Olivier Rais; Axelle Durand-Hermouet; Caroline Hervet; Olivier Plantard; Claude Rispe


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  <identifier identifierType="DOI">10.5281/zenodo.1137702</identifier>
  <creators>
    <creator>
      <creatorName>N Pierre Charrier</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5681-0091</nameIdentifier>
      <affiliation>INRA</affiliation>
    </creator>
    <creator>
      <creatorName>Marjorie Couton</creatorName>
      <affiliation>INRA</affiliation>
    </creator>
    <creator>
      <creatorName>Maarten J Voordouw</creatorName>
      <affiliation>Université de Neuchâtel</affiliation>
    </creator>
    <creator>
      <creatorName>Olivier Rais</creatorName>
      <affiliation>Université de Neuchâtel</affiliation>
    </creator>
    <creator>
      <creatorName>Axelle Durand-Hermouet</creatorName>
      <affiliation>INRA</affiliation>
    </creator>
    <creator>
      <creatorName>Caroline Hervet</creatorName>
      <affiliation>INRA</affiliation>
    </creator>
    <creator>
      <creatorName>Olivier Plantard</creatorName>
      <affiliation>INRA</affiliation>
    </creator>
    <creator>
      <creatorName>Claude Rispe</creatorName>
      <affiliation>INRA</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Annotation table - Whole body transcriptomes of the tick Ixodes ricinus at different stage and feeding conditions</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2017</publicationYear>
  <subjects>
    <subject>Ixodes ricinus, RNA-Seq, De novo assembly, Expression profiling, Polymorphism</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2017-08-01</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1137702</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.832278</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Annotation table for a &lt;em&gt;de novo&lt;/em&gt; assembled transcriptome of&lt;em&gt; Ixodes ricinus&lt;/em&gt; in different stages and conditions.&lt;/p&gt;

&lt;p&gt;Description of the fields of each column (Trinotate results, and additionnal statistics):&lt;/p&gt;

&lt;p&gt;1. Contig_name:&amp;nbsp; name of the contig (Trinity assembly)&lt;/p&gt;

&lt;p&gt;2. sprot_Top_BLASTX_hit: first hit of the blastx search against SwissProt (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/)&lt;/p&gt;

&lt;p&gt;3. TrEMBL_Top_BLASTX_hit: first hit of the blastx search against Uniref90 (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/)&lt;/p&gt;

&lt;p&gt;4. RNAMMER: identification of non-coding RNAs&lt;/p&gt;

&lt;p&gt;5. prot_id: identifier of the predicted protein (TransDecoder)&lt;/p&gt;

&lt;p&gt;6. prot_coords: coordinates (start, end and strand) of the predicted protein on the contig&lt;/p&gt;

&lt;p&gt;7. sprot_Top_BLASTP_hit: first hit of the blastp search between the predicted protein and SwissProt (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/)&lt;/p&gt;

&lt;p&gt;8. TrEMBL_Top_BLASTP_hit: first hit of the blastp search between the predicted protein and Uniref90 (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/)&lt;/p&gt;

&lt;p&gt;9. Pfam: result of the search against PfamA database&lt;/p&gt;

&lt;p&gt;10. SignalP: prediction of a signal peptide with SignalP&lt;/p&gt;

&lt;p&gt;11. TmHMM: prediction of a transmembrane domain with THMM&lt;/p&gt;

&lt;p&gt;12. eggnog: eggNOG database of orthologous genes (v3.0) assignation&lt;/p&gt;

&lt;p&gt;13. gene_ontology_blast: GO assignation based on blast results&lt;/p&gt;

&lt;p&gt;14. gene_ontology_pfam: GO assignation based on pfam results&lt;/p&gt;

&lt;p&gt;15. Contig_length: length of the contig in bp&lt;/p&gt;

&lt;p&gt;16. Busco_Id: name of the BUSCO (v1)&lt;/p&gt;

&lt;p&gt;17. Busco_status: status of the BUSCO (complete/fragmented/duplicated)&lt;/p&gt;

&lt;p&gt;18-32: Kallisto read counts for the 15 libraries&lt;/p&gt;

&lt;p&gt;A, B, C: unfed nymphs (replicates 1, 2, 3)&lt;/p&gt;

&lt;p&gt;D, E, F:&amp;nbsp; partially fed nymphs (replicates 1, 2, 3)&lt;/p&gt;

&lt;p&gt;G, H, I: males (unfed) (replicates 1, 2, 3)&lt;/p&gt;

&lt;p&gt;J, K, L: unfed adult females (replicates 1, 2, 3)&lt;/p&gt;

&lt;p&gt;M, N, O:&amp;nbsp; partially fed adult females (replicates 1, 2, 3)&lt;/p&gt;

&lt;p&gt;33. log2FoldChange_UnfedVsPartiallyFed:&amp;nbsp; log fold change in base 2 of expression (comparison between &amp;quot;unfed&amp;quot; -including males- and &amp;quot;fed&amp;quot; ticks)&lt;/p&gt;

&lt;p&gt;34. pvalue_UnfedVsPartiallyFed: p-value of the comparison between &amp;quot;unfed&amp;quot; -including males- and &amp;quot;fed&amp;quot; ticks&lt;/p&gt;

&lt;p&gt;35. log2FoldChange_MaleVsFemale: log fold change in base 2 of expression (comparison between &amp;quot;males&amp;quot; and &amp;quot;females&amp;quot;)&lt;/p&gt;

&lt;p&gt;36. pvalue_MaleVsFemale: p-value of the comparison between &amp;quot;males&amp;quot; and &amp;quot;females&amp;quot;&lt;/p&gt;

&lt;p&gt;37. log2FoldChange_NymphsVsAdults: log fold change in base 2 of expression (comparison between &amp;quot;nymphs&amp;quot; and &amp;quot;adults&amp;quot; -males and females-)&lt;/p&gt;

&lt;p&gt;38. pvalue_NymphsVsAdults: p-value of the comparison between &amp;quot;nymphs&amp;quot; and &amp;quot;adults&amp;quot; -males and females-)&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
    <description descriptionType="Other">Fixed column 8 (blastp result on TrEMBL)</description>
  </descriptions>
</resource>
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