MOESM1 of Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

Additional file 1. This file contains all supplementary tables relating to the characterisation of sheep lncRNAs. Table S1. Candidate sheep lncRNAs: a shortlist of novel gene models (plus independently confirmed known gene models) assessed for coding potential using CPC, CPAT, PLEK, blastp vs. Swiss-Prot, and HMMER vs. Pfam. Table S4. Sheep gene models considered as non-coding by either CPC, CPAT or PLEK but showing sequence homology to either a known protein (in Swiss-Prot) or protein domain (in Pfam-A). Table S6. Number of novel sheep lncRNA gene models identified per chromosome. Table S8. Number of novel sheep lncRNA gene models identified, by category. Table S10. Alignments of novel sheep lncRNA gene models to goat, cattle and human lncRNA. Table S19. Expression level estimates for 13,047 novel sheep lncRNAs, as transcripts per million (TPM), which were assessed using 71 adult RNA-seq libraries (11 tissues plus one cell type under two conditions, each sample is sequenced for six individuals). Table S21. Reproducibility of sheep lncRNA gene models when merging all combinations of data from six adults (three females and three males), for each individual a common set of RNA-seq libraries (comprising 31 tissues/cell types) was available. Table S22. Number of sheep expression atlas RNA-seq libraries (out of 429 in total) for which a candidate lncRNA gene model cannot be fully reconstructed. Table S23. Genes within each co-expression cluster, after network analysis of the sheep RNA-seq libraries. Table S24. Number of sheep lncRNAs co-expressed with protein-coding genes. Table S25. Distance between lncRNAs and protein-coding genes within the same co-expression cluster, on the same chromosome, for sheep. Table S26. Correlation between the expression profile of sheep lncRNAs and their nearest protein-coding genes, both 5′ and 3′.