Dataset Open Access

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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    <subfield code="a">&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;

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