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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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    "description": "<p>Annotation table for a <em>de novo</em> assembled transcriptome of<em> Ixodes ricinus</em> in different stages and conditions.</p>\n\n<p>Description of the fields of each column (Trinotate results, and additionnal statistics):</p>\n\n<p>1. Contig_name:&nbsp; name of the contig (Trinity assembly)</p>\n\n<p>2. sprot_Top_BLASTX_hit: first hit of the blastx search against SwissProt (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/)</p>\n\n<p>3. TrEMBL_Top_BLASTX_hit: first hit of the blastx search against Uniref90 (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/)</p>\n\n<p>4. RNAMMER: identification of non-coding RNAs</p>\n\n<p>5. prot_id: identifier of the predicted protein (TransDecoder)</p>\n\n<p>6. prot_coords: coordinates (start, end and strand) of the predicted protein on the contig</p>\n\n<p>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/)</p>\n\n<p>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/)</p>\n\n<p>9. Pfam: result of the search against PfamA database</p>\n\n<p>10. SignalP: prediction of a signal peptide with SignalP</p>\n\n<p>11. TmHMM: prediction of a transmembrane domain with THMM</p>\n\n<p>12. eggnog: eggNOG database of orthologous genes (v3.0) assignation</p>\n\n<p>13. gene_ontology_blast: GO assignation based on blast results</p>\n\n<p>14. gene_ontology_pfam: GO assignation based on pfam results</p>\n\n<p>15. Contig_length: length of the contig in bp</p>\n\n<p>16. Busco_Id: name of the BUSCO (v1)</p>\n\n<p>17. Busco_status: status of the BUSCO (complete/fragmented/duplicated)</p>\n\n<p>18-32: Kallisto read counts for the 15 libraries</p>\n\n<p>A, B, C: unfed nymphs (replicates 1, 2, 3)</p>\n\n<p>D, E, F:&nbsp; partially fed nymphs (replicates 1, 2, 3)</p>\n\n<p>G, H, I: males (unfed) (replicates 1, 2, 3)</p>\n\n<p>J, K, L: unfed adult females (replicates 1, 2, 3)</p>\n\n<p>M, N, O:&nbsp; partially fed adult females (replicates 1, 2, 3)</p>\n\n<p>33. log2FoldChange_UnfedVsPartiallyFed:&nbsp; log fold change in base 2 of expression (comparison between &quot;unfed&quot; -including males- and &quot;fed&quot; ticks)</p>\n\n<p>34. pvalue_UnfedVsPartiallyFed: p-value of the comparison between &quot;unfed&quot; -including males- and &quot;fed&quot; ticks</p>\n\n<p>35. log2FoldChange_MaleVsFemale: log fold change in base 2 of expression (comparison between &quot;males&quot; and &quot;females&quot;)</p>\n\n<p>36. pvalue_MaleVsFemale: p-value of the comparison between &quot;males&quot; and &quot;females&quot;</p>\n\n<p>37. log2FoldChange_NymphsVsAdults: log fold change in base 2 of expression (comparison between &quot;nymphs&quot; and &quot;adults&quot; -males and females-)</p>\n\n<p>38. pvalue_NymphsVsAdults: p-value of the comparison between &quot;nymphs&quot; and &quot;adults&quot; -males and females-)</p>\n\n<p>&nbsp;</p>\n\n<p>&nbsp;</p>", 
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    "title": "Annotation table - Whole body transcriptomes of the tick Ixodes ricinus at different stage and feeding conditions", 
    "notes": "Fixed column 8 (blastp result on TrEMBL)", 
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    "keywords": [
      "Ixodes ricinus, RNA-Seq, De novo assembly, Expression profiling, Polymorphism"
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    "publication_date": "2017-08-01", 
    "creators": [
      {
        "orcid": "0000-0002-5681-0091", 
        "affiliation": "INRA", 
        "name": "N Pierre Charrier"
      }, 
      {
        "affiliation": "INRA", 
        "name": "Marjorie Couton"
      }, 
      {
        "affiliation": "Universit\u00e9 de Neuch\u00e2tel", 
        "name": "Maarten J Voordouw"
      }, 
      {
        "affiliation": "Universit\u00e9 de Neuch\u00e2tel", 
        "name": "Olivier Rais"
      }, 
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        "affiliation": "INRA", 
        "name": "Axelle Durand-Hermouet"
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        "affiliation": "INRA", 
        "name": "Caroline Hervet"
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        "affiliation": "INRA", 
        "name": "Olivier Plantard"
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        "affiliation": "INRA", 
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