August 1, 2017 Dataset Open Access

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

JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/8e91fa29-4f14-40aa-9642-013989bc8aa3/Ixodes-ricinus_de_novo_transcriptome_Trinotate_BUSCO_and_DE_updateUniref90.tsv"
      }, 
      "checksum": "md5:a30cf263332170225f5cb064c7fd575a", 
      "bucket": "8e91fa29-4f14-40aa-9642-013989bc8aa3", 
      "key": "Ixodes-ricinus_de_novo_transcriptome_Trinotate_BUSCO_and_DE_updateUniref90.tsv", 
      "type": "tsv", 
      "size": 92607281
    }
  ], 
  "owners": [
    34064
  ], 
  "doi": "10.5281/zenodo.1137702", 
  "stats": {
    "version_unique_downloads": 26.0, 
    "unique_views": 102.0, 
    "views": 107.0, 
    "version_views": 129.0, 
    "unique_downloads": 24.0, 
    "version_unique_views": 121.0, 
    "volume": 2593003868.0, 
    "version_downloads": 30.0, 
    "downloads": 28.0, 
    "version_volume": 2779800551.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.1137702", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.832278", 
    "bucket": "https://zenodo.org/api/files/8e91fa29-4f14-40aa-9642-013989bc8aa3", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.832278.svg", 
    "html": "https://zenodo.org/record/1137702", 
    "latest_html": "https://zenodo.org/record/1137702", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.1137702.svg", 
    "latest": "https://zenodo.org/api/records/1137702"
  }, 
  "conceptdoi": "10.5281/zenodo.832278", 
  "created": "2018-01-08T14:21:20.827589+00:00", 
  "updated": "2020-01-24T19:23:44.322963+00:00", 
  "conceptrecid": "832278", 
  "revision": 4, 
  "id": 1137702, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.1137702", 
    "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>", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "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)", 
    "relations": {
      "version": [
        {
          "count": 2, 
          "index": 1, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "832278"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "1137702"
          }
        }
      ]
    }, 
    "keywords": [
      "Ixodes ricinus, RNA-Seq, De novo assembly, Expression profiling, Polymorphism"
    ], 
    "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"
      }, 
      {
        "affiliation": "INRA", 
        "name": "Axelle Durand-Hermouet"
      }, 
      {
        "affiliation": "INRA", 
        "name": "Caroline Hervet"
      }, 
      {
        "affiliation": "INRA", 
        "name": "Olivier Plantard"
      }, 
      {
        "affiliation": "INRA", 
        "name": "Claude Rispe"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.832278", 
        "relation": "isVersionOf"
      }
    ]
  }
}