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

Dublin Core Export

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  <dc:creator>N Pierre Charrier</dc:creator>
  <dc:creator>Marjorie Couton</dc:creator>
  <dc:creator>Maarten J Voordouw</dc:creator>
  <dc:creator>Olivier Rais</dc:creator>
  <dc:creator>Axelle Durand-Hermouet</dc:creator>
  <dc:creator>Caroline Hervet</dc:creator>
  <dc:creator>Olivier Plantard</dc:creator>
  <dc:creator>Claude Rispe</dc:creator>
  <dc:date>2017-08-01</dc:date>
  <dc:description>Annotation table for a de novo assembled transcriptome of Ixodes ricinus in different stages and conditions.

Description of the fields of each column (Trinotate results, and additionnal statistics):

1. Contig_name:  name of the contig (Trinity assembly)

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

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

4. RNAMMER: identification of non-coding RNAs

5. prot_id: identifier of the predicted protein (TransDecoder)

6. prot_coords: coordinates (start, end and strand) of the predicted protein on the contig

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/)

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/)

9. Pfam: result of the search against PfamA database

10. SignalP: prediction of a signal peptide with SignalP

11. TmHMM: prediction of a transmembrane domain with THMM

12. eggnog: eggNOG database of orthologous genes (v3.0) assignation

13. gene_ontology_blast: GO assignation based on blast results

14. gene_ontology_pfam: GO assignation based on pfam results

15. Contig_length: length of the contig in bp

16. Busco_Id: name of the BUSCO (v1)

17. Busco_status: status of the BUSCO (complete/fragmented/duplicated)

18-32: Kallisto read counts for the 15 libraries

A, B, C: unfed nymphs (replicates 1, 2, 3)

D, E, F:  partially fed nymphs (replicates 1, 2, 3)

G, H, I: males (unfed) (replicates 1, 2, 3)

J, K, L: unfed adult females (replicates 1, 2, 3)

M, N, O:  partially fed adult females (replicates 1, 2, 3)

33. log2FoldChange_UnfedVsPartiallyFed:  log fold change in base 2 of expression (comparison between "unfed" -including males- and "fed" ticks)

34. pvalue_UnfedVsPartiallyFed: p-value of the comparison between "unfed" -including males- and "fed" ticks

35. log2FoldChange_MaleVsFemale: log fold change in base 2 of expression (comparison between "males" and "females")

36. pvalue_MaleVsFemale: p-value of the comparison between "males" and "females"

37. log2FoldChange_NymphsVsAdults: log fold change in base 2 of expression (comparison between "nymphs" and "adults" -males and females-)

38. pvalue_NymphsVsAdults: p-value of the comparison between "nymphs" and "adults" -males and females-)

 

 </dc:description>
  <dc:description>Fixed column 8 (blastp result on TrEMBL)</dc:description>
  <dc:identifier>https://zenodo.org/record/1137702</dc:identifier>
  <dc:identifier>10.5281/zenodo.1137702</dc:identifier>
  <dc:identifier>oai:zenodo.org:1137702</dc:identifier>
  <dc:relation>doi:10.5281/zenodo.832278</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>Ixodes ricinus, RNA-Seq, De novo assembly, Expression profiling, Polymorphism</dc:subject>
  <dc:title>Annotation table - Whole body transcriptomes of the tick Ixodes ricinus at different stage and feeding conditions</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
</oai_dc:dc>