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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.

DOI: 10.7287/peerj.preprints.286v1/supp-1

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.

DOI: 10.7287/peerj.preprints.286v1/supp-2

Supplemental File S2: S2_Cufflinks_assembly.gtf.gz

Annotation of the individual pre-consensus horse Cufflinks assembly.

DOI: 10.7287/peerj.preprints.286v1/supp-3

Supplemental File S3: S3_Scripture_assembly.gtf.gz

Annotation of the individual pre-consensus horse Scripture assembly.

DOI: 10.7287/peerj.preprints.286v1/supp-4

Supplemental File S4: S4_UoN_horse_consensus_assembly.gtf.gz

Annotation of the University of Nottingham (UoN) final consensus horse assembly.

DOI: 10.7287/peerj.preprints.286v1/supp-5

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).

DOI: 10.7287/peerj.preprints.286v1/supp-6

Supplemental File S6: S6_UoN_horse_cDNA_sequences.fa.gz

University of Nottingham (UoN) consensus horse cDNA sequences.

DOI: 10.7287/peerj.preprints.286v1/supp-7

Supplemental File S7: S7_Ensembl71_genes_RPKMs_UoN-reads.xls

RPKM values for all Ensembl v71 genes.

DOI: 10.7287/peerj.preprints.286v1/supp-8

Supplemental File S8: S8_sample-enriched-genes.zip

Tables containing the sample enriched Ensembl v71 gene IDs.

DOI: 10.7287/peerj.preprints.286v1/supp-9

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).

DOI: 10.7287/peerj.preprints.286v1/supp-10

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.

DOI: 10.7287/peerj.preprints.286v1/supp-11

Supplemental File S11: S11_species_UoN_numTopHits_BLASTX.xls

Table showing the number of top hit BLASTX hits for each species.

DOI: 10.7287/peerj.preprints.286v1/supp-12

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.

DOI: 10.7287/peerj.preprints.286v1/supp-13

Additional Information

Competing Interests

Richard D Emes is an Academic Editor for PeerJ.

Author Contributions

Joanna Moreton conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Sunir Malla performed the experiments, wrote the paper, reviewed drafts of the paper.

Aziz Aboobaker conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Rachael Tarlinton contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Richard D Emes conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

(1) Home Office and local Ethical Approval Committee (PPL 40/3354) (2) Institutional Animal Care and Use Committee of Cornell University, protocol # 1986-0216

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The database and accession number will be provided prior to publication after peer review.

Funding

Funding for this project was provided by the University of Nottingham. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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