Characterisation of the horse transcriptome from immunologically active tissues
- Published
- Accepted
- Subject Areas
- Bioinformatics
- Keywords
- Equus caballus, RNA-Seq, transcriptome assembly
- Copyright
- © 2014 Moreton et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. Characterisation of the horse transcriptome from immunologically active tissues. PeerJ PrePrints 2:e286v1 https://doi.org/10.7287/peerj.preprints.286v1
Abstract
The immune system of the horse has not been well studied, despite the fact that the horse displays several features such as sensitivity to bacterial lipopolysaccharide that make them in many ways a more suitable model of some human disorders than the current rodent models. The difficulty of working with large animal models has however limited characterisation of gene expression in the horse immune system with current annotations for the equine genome restricted to predictions from other mammals and the few described horse proteins. This paper outlines sequencing of 184 million transcriptome short reads from immunologically active tissues of three horses including the genome reference “Twilight”. In a comparison with the Ensembl horse genome annotation, we found 8,763 potentially novel isoforms.
Supplemental Information
Figure 1 : Hierarchical clustering of gene expression profiles in 7 tissues
The R command “hclust” was used for the hierarchical clustering analysis. The branch values are the pvclust approximately unbiased (AU) p-values (left) and bootstrap (BP) probability values (right) where the p-values are expressed as percentages.
Supplemental File 1: S1_CLC_SOLiD_trim_adapter_list.xls
The trim adapter list used in CLC with SOLiD adapter sequences and single-base-repeat sequences.
Supplemental File S2: S2_Cufflinks_assembly.gtf.gz
Annotation of the individual pre-consensus horse Cufflinks assembly.
Supplemental File S3: S3_Scripture_assembly.gtf.gz
Annotation of the individual pre-consensus horse Scripture assembly.
Supplemental File S4: S4_UoN_horse_consensus_assembly.gtf.gz
Annotation of the University of Nottingham (UoN) final consensus horse assembly.
Supplemental File S5: S5_Ensembl-vs-UoN_Cuffcompare-results.xls
Table of Cuffcompare results showing the similarities between the University of Nottingham (UoN) consensus assembly and the Ensembl annotations (using Ensembl as a Cuffcompare reference).
Supplemental File S6: S6_UoN_horse_cDNA_sequences.fa.gz
University of Nottingham (UoN) consensus horse cDNA sequences.
Supplemental File S7: S7_Ensembl71_genes_RPKMs_UoN-reads.xls
RPKM values for all Ensembl v71 genes.
Supplemental File S8: S8_sample-enriched-genes.zip
Tables containing the sample enriched Ensembl v71 gene IDs.
Supplemental File S9: S9_Ensembl-vs-UoN_Cuffcompare-results_UoN-as-ref.xls
Table of Cuffcompare results showing the similarities between the University of Nottingham (UoN) consensus assembly and the Ensembl annotations (using UoN as a Cuffcompare reference).
Supplemental File S10: S10_Ensembl-vs-UoN_Cuffcompare-results_PFAM-GO-BLASTX.xls
Table of Cuffcompare results showing the similarities between the University of Nottingham (UoN) consensus assembly and Ensembl. The number of annotated UoN transcripts for each of the Cuffcompare categories is also shown.
Supplemental File S11: S11_species_UoN_numTopHits_BLASTX.xls
Table showing the number of top hit BLASTX hits for each species.
Supplemental File S12: S12_top10-GO-names_sample-enriched-genes.xls
Table showing the top ten gene ontology (GO) term names for the sample-enriched genes.