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1 Supplemental Data Legends Supplemental Table S1. Entrez gene symbol, Affymetrix probe ID, gene description, P value and fold change differences for differentially expressed genes (DEGs) in the endometrium of cyclic heifers with high compared to normal P4 concentrations on Day 5 (A), Day 7 (B), Day 13 (C), and Day 16 (D) of the estrous cycle. Fold change differences reflect changes in cyclic high P4 compared to cyclic normal P4. Supplemental Table S2. Entrez gene symbol, Affymetrix probe ID, gene description, P value and fold change differences for differentially expressed genes (DEGs) in the endometrium on Day 5 compared to Day 7 of the estrous cycle in heifers with (A) normal and high P4 concentrations, (B) heifers with normal P4 concentration only and (C) heifers with high P4 concentration. Fold change differences reflect changes on Day 5 compared to Day 7. Supplemental Table S3. Entrez gene symbol, Affymetrix probe ID, gene description, P value and fold change differences for differentially expressed genes (DEGs) in the endometrium on Day 7 compared to Day 13 of the estrous cycle in heifers with (A) normal and high P4 concentrations, (B) heifers with normal P4 concentration only and (C) heifers with high P4 concentration. Fold change differences reflect changes on Day 7 compared to Day 13. Supplemental Table S4. Entrez gene symbol, Affymetrix probe ID, gene description, P value and fold change differences for differentially expressed genes (DEGs) in the endometrium on Day 13 compared to Day 16 of the estrous cycle in heifers with (A) normal and high P4 concentrations, (B) heifers with normal P4 concentration only and (C) heifers with high P4 concentration. Fold change differences reflect changes on Day 13 compared to Day 16. Supplemental Figure S1. Graphical representation of ingenuity pathway interaction network analysis. Differentially expressed genes between Day 5 and 7 of the estrous cycle in heifers with high P4 were involved the interaction networks (A) Cell Cycle, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair, (B) Cell Cycle, Cellular Movement, Cancer, (C) Cell Cycle, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair and (D) DNA Replication, Recombination, and Repair, Cell Cycle, Cellular Assembly and Organization. These DEGs are displayed as colored shapes with the grey nodes indicative of protein complexes and/or non-specified members of a gene family which are important components of the interaction network between these DEGs. The network displays nodes (genes/ gene products) and edges (the biological relationship between nodes). The color intensity of the nodes indicates the fold change increase (red) or decrease (green) associated with a particular gene on Day 7 compared with Day 5. A solid line indicates a direct interaction between nodes (genes/ gene products) and a dashed line indicates an indirect relationship between nodes. The shape of the node is indicative of its function (See Supplemental Key). Supplemental Figure S2. Graphical representation of ingenuity pathway interaction network analysis. Differentially expressed genes between Day 7 and 13 of the estrous cycle in heifers with normal P4 were involved the interaction networks (A) Lipid Metabolism, Molecular Transport, Small Molecule Biochemistry, (B) Cell Cycle, Embryonic Development, Renal and Urological System Development and Function, (C) Carbohydrate Metabolism, Embryonic

2 Development, Organ Development, (D) Cancer, Gastrointestinal Disease, Cellular Development and (E) Cellular Development, Cellular Growth and Proliferation, Connective Tissue Development and Function. These DEGs are displayed as colored shapes with the grey nodes indicative of protein complexes and/or non-specified members of a gene family which are important components of the interaction network between these DEGs. The network displays nodes (genes/ gene products) and edges (the biological relationship between nodes). The color intensity of the nodes indicates the fold change increase (red) or decrease (green) associated with a particular gene on Day 13 compared with Day 7. A solid line indicates a direct interaction between nodes (genes/ gene products) and a dashed line indicates an indirect relationship between nodes. The shape of the node is indicative of its function (See Supplemental Key). Supplemental Figure S3. Graphical representation of ingenuity pathway interaction network analysis. Differentially expressed genes between Day 7 and 13 of the estrous cycle in heifers with high P4 were involved the interaction networks (A) Cellular Movement, Carbohydrate Metabolism, Cell-To-Cell Signaling and Interaction, (B) Lipid Metabolism, Small Molecule Biochemistry, Vitamin and Mineral Metabolism, (C) Cell Cycle, Cellular Development, Tumor Morphology, (D) Renal Tubule Injury, Genetic Disorder, Hematological System Development and Function and (E) Carbohydrate Metabolism, Small Molecule Biochemistry, Cell Death. These DEGs are displayed as colored shapes with the grey nodes indicative of protein complexes and/or non-specified members of a gene family which are important components of the interaction network between these DEGs. The network displays nodes (genes/ gene products) and edges (the biological relationship between nodes). The color intensity of the nodes indicates the fold change increase (red) or decrease (green) associated with a particular gene on Day 13 compared with Day 7. A solid line indicates a direct interaction between nodes (genes/ gene products) and a dashed line indicates an indirect relationship between nodes. The shape of the node is indicative of its function (See Supplemental Key). Supplemental Figure S4. Graphical representation of ingenuity pathway interaction network analysis. Differentially expressed genes between Day 13 and 16 of the estrous cycle in heifers with normal P4 were involved the interaction networks (A) Lipid Metabolism, Small Molecule Biochemistry, Molecular Transport, (B) Tissue Development, Cellular Growth and Proliferation, Lymphoid Tissue Structure and Development and (C) Lipid Metabolism, Molecular Transport, Small Molecule Biochemistry. These DEGs are displayed as colored shapes with the grey nodes indicative of protein complexes and/or non-specified members of a gene family which are important components of the interaction network between these DEGs. The network displays nodes (genes/ gene products) and edges (the biological relationship between nodes). The color intensity of the nodes indicates the fold change increase (red) or decrease (green) associated with a particular gene on Day 16 compared with Day 13. A solid line indicates a direct interaction between nodes (genes/ gene products) and a dashed line indicates an indirect relationship between nodes. The shape of the node is indicative of its function (See Supplemental Key).

3 Supplemental Figure S1 (A)

4 (B)

5 (C)

6 (D)

7 Supplemental Figure S2 (A)

8 (B)

9 (C)

10 (D)

11 (E)

12 Supplemental Figure S3 (A)

13 (B)

14 (C)

15 (D)

16 (E)

17 Supplemental Figure S4 (A)

18 (B)

19 (C)

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