Additional file 3: Table S3. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Differentially expressed genes obtained between high and low genomic breeding value groups for backfat thickness in Nellore steers with FDR 10%. The table contains the Ensembl gene identification, gene symbol, mean normalized counts, Log2 fold Change from low to high group, p value and p value adjusted for a false discovery rate of 10%. (XLS 31 kb

Additional file 2: Table S2. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Differentially expressed genes obtained between high and low genomic breeding value groups for ribeye area in Nellore steers with FDR 10%. The table contains the Ensembl gene identification, gene symbol, mean normalized counts, Log2 fold Change from low to high group, p value and p value adjusted for a false discovery rate of 10%. (XLS 45 kb

Additional file 5: Table S5. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Correspondence between sample names and European Nucleotide Archive (ENA) identifier (accession PRJEB13188 and PRJEB19421). (XLS 29 kb

Additional file 7: Figures S3 and S4. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Histogram of p-values from RNA-Seq data of Longissimus dorsi muscle of Nellore steers by DESeq2 software, for ribeye area and backfat thickness. Y-axis represents the frequency of p-values and x-axis represents the residual of p-values. (PDF 108 kb

Additional file 1: Table S1. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Test of means (t-test) of intramuscular fat (IMF), backfat thickness (BFT) and ribeye area (REA) between groups with High and Low REA and BFT in the Longissimus dorsi muscle of Nellore steers. (XLS 33 kb

Additional file 6: Figures S1 and S2. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Plots of dispersion estimates of all ribeye area and backfat thickness genes. The black dots are the dispersion estimates of the empirical values of each gene; the red line represents the trend line; the blue dots represent the genes estimates regressed through the trend line used in the hypothesis test; and the blue circles above the “cloud” of points are genes which have high gene-wise dispersion estimates which are labelled as dispersion outliers, and will not be used in the hypothesis test. (PDF 110 kb

Additional file 14: Tables S18, S19, S20 and S21. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

Gene ontology (GO) enrichment analysis by Cytoscape of genes in mRNA modules negatively correlated with miRNA modules: enrichment of genes from mRNA modules constructed in the High intramuscular fat (IMF) group (Table S18) and in the Low IMF group (Table S19). Gene ontology enrichment analysis by Cytoscape of target genes of hub miRNAs in modules negatively correlated with mRNA modules: enrichment of target genes of miRNA modules constructed in the High IMF group (Table S20) and in the Low IMF group (Table S21). The table contains the module’s name, gene ontology ID, p-value and adjusted p-value of GO, the description of them and the genes present in each biological process enriched. (XLSX 71 kb

Additional file 18: Figure S9. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

Scale free topology model and mean connectivity of the mRNA networks based on the power value β. (A) H group. (B) L group. (PDF 92 kb

Manifesto. Il Commendatore F. D. Gio. Secondo Canalis di Cumiana, generale d'infanteria nelle armate di S. R. M., e governatore della presente città e sua provincia

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Additional file 17: Tables S22, S23, S24 and S25. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

Gene ontology (GO) enrichment analysis by Cytoscape of genes in mRNA modules correlated with the intramuscular fat (IMF) trait: enrichment of genes from mRNA modules correlated with High IMF (Table S22) and Low IMF groups (Table S23). Gene ontology enrichment analysis by Cytoscape of target genes of hub miRNAs in modules correlated with the IMF trait: enrichment of target genes of miRNA modules correlated with High intramuscular fat (Table S24) and Low IMF groups (Table S25). The table contains module’s name, gene ontology ID, p-value and adjusted p-value of GO, the description of them and the genes present in each biological process enriched. (XLSX 98 kb