Fig 1.
Diagram showing RNA-seq bioinformatics and statistical analysis.
The main workflow steps and their order are shown. These computational workflows are available at https://github.com/carolcorreia/Estrus-Endometrium-RNA-sequencing.
Fig 2.
Visualisation of significantly differentially expressed genes (DEGs).
A) The number of DEGs with increased and decreased expression at each perioestrus time point, relative to expression at the oestrus time point is shown. B) Venn diagram of numbers of DEGs for the five perioestrus time points relative to oestrus.
Table 1.
Top DEGs in bovine endometrium at 12 h post-CIDR removal versus oestrus, ranked by ascending B-H FDR.
Table 2.
Top DEGs in bovine endometrium at 24 h post-CIDR removal versus oestrus, ranked by ascending B-H FDR.
Table 3.
Top DEGs in bovine endometrium at 12 h post-oestrus versus oestrus, ranked by ascending B-H FDR.
Table 4.
Top DEGs in bovine endometrium at 48 h post-oestrus versus oestrus, ranked by ascending B-H FDR.
Table 5.
Top DEGs in bovine endometrium at Day 7 post-oestrus (luteal phase) versus oestrus, ranked by ascending B-H FDR.
Table 6.
Top five diseases and functions categories and canonical pathways based on DEGs from each perioestrous time point versus the onset of oestrus.
Fig 3.
IPA analysis showing the over-represented canonical pathways at the five time points relative to oestrus.
Pathways associated with significantly modulated genes are shown on the x axis of each bar graph and the -log significance is shown on the y axis. The functions are listed from most significant to less significant (indicated by bar height). Orange bars denote a positive z score, blue bars denote a negative z score. An orange horizontal line denotes the threshold for significance, i.e. p = 0.05. The ratios, which are the number of genes that are modulated in a given pathway divided by the total number of genes in the pathway, are shown on the right-hand side y axis. A) 12 h post-CIDR removal, B) 24 h post-CIDR removal, C) 12 h post-oestrus, D) 48 h post-oestrus, E) Day 7 post-oestrus (luteal phase).
Fig 4.
Top IPA gene interaction network at 12 h post-CIDR removal versus oestrus.
Network 1 is involved in Endocrine system disorders, Hereditary disorders, and Organismal injury and abnormalities (score 34, with 27 focus molecules). The relationship is described as either a direct interaction (solid line) or an indirect interaction (dashed line), whereas the intensity of the colour indicates the level of upregulation (red) or downregulation (green) of the respective molecules. Reprinted from Qiagen IPA under a CC BY license, with permission from Qiagen, original copyright 2017.
Fig 5.
Top IPA gene interaction network at 24 h post-CIDR removal versus oestrus.
Network 1 is involved in Neurological disease, Nervous System Development and Function and Behaviour (score 45, with 26 focus molecules). The relationship is described as either a direct interaction (solid line) or an indirect interaction (dashed line), whereas the intensity of the colour indicates the level of upregulation (red) or downregulation (green) of the respective molecules. Reprinted from Qiagen IPA under a CC BY license, with permission from Qiagen, original copyright 2017.
Fig 6.
Top IPA gene interaction network at 12 h post-oestrus versus oestrus.
Network 1 is involved in Organ Development, Reproductive System Development and Function and Cell Death and Survival (score 40, with 17 focus molecules). The relationship is described as either a direct interaction (solid line) or an indirect interaction (dashed line), whereas the intensity of the colour indicates the level of upregulation (red) or downregulation (green) of the respective molecules. Reprinted from Qiagen IPA under a CC BY license, with permission from Qiagen, original copyright 2017.
Fig 7.
Top IPA gene interaction network at 48 h post-oestrus versus oestrus.
Network 1 is involved in Connective Tissue Disorders, Developmental Disorder and Hereditary Disorder (score 44, with 32 focus molecules). The relationship is described as either a direct interaction (solid line) or an indirect interaction (dashed line), whereas the intensity of the colour indicates the level of upregulation (red) or downregulation (green) of the respective molecules. Reprinted from Qiagen IPA under a CC BY license, with permission from Qiagen, original copyright 2017.
Fig 8.
Top IPA gene interaction network at Day 7 post-oestrus (luteal phase) versus oestrus.
Network 1 is involved in Cellular Assembly and Organization, Developmental Disorder, Nervous System Development and Function (score 32, with 35 focus molecules). The relationship is described as either a direct interaction (solid line) or an indirect interaction (dashed line), whereas the intensity of the colour indicates the level of upregulation (red) or downregulation (green) of the respective molecules. Reprinted from Qiagen IPA under a CC BY license, with permission from Qiagen, original copyright 2017.
Table 7.
The five top IPA upstream regulators, based on DEGs from each of the perioestrous time points versus the onset of oestrus.