Figure 1

Work flow for next generation sequencing data analysis, the resulting gene expression output from TMM EdgeR and downstream analysis with differentially expressed genes. Sequenced reads were mapped to the bovine genome with TopHat, summarised with HtSeq Count and normalised with TMM EdgeR. Output files of differentially expressed (DE) genes with P < 0.05 (adjusted P < 0.45) and an adjusted P < 0.1 were used in GoSeq pathway analysis. Nineteen of the most highly significant DE genes, (adjusted P < 0.1) 15 days and 30 days postpartum, were selected for assessment by qRT-PCR in a larger sample set (n = 5).