Inah Camaya PhD Thesis - Supplementary Data

Supplementary files for the PhD thesis of Inah Camaya, relating to the analysis of
(1) the differential abundance of proteins in the pancreas of NOD mice treated with FhHDM-1,
(2) the differential expression of mRNA in beta cells treated with FhHDM-1 under basal and apoptotic conditions and,
(3) the differential expression of miRNA:mRNA in beta cells treated with FhHDM-1 under basal and apoptotic conditions. Supplementary Figure 2.1. Interlinked contiguous quartet of interacting proteins (Cdh1, Agt, Rps6kb1, and Bmi1)
Supplementary Table 2.1. LC-MS/MS identification of proteins in NOD mouse pancreas
Supplementary Table 2.2. Proteins identified in the pancreas of mice
Supplementary Table 2.3. Interrogation of the protein network using specific search terms
Supplementary Table 2.4. Differentially expressed genes with a logarithmic fold change of >1 or <1, and a false discovery rate <0.05 in NIT-1 β-cells treated with FhHDM-1 as compared to untreated cells
Supplementary Table 3.1. Proteins with significantly different abundance in FhHDM-1 treated β-cells compared to untreated controls
Supplementary Table 4.1. Predicted gene targets for differentially expressed miRNAs in FhHDM-1 treated β-cells compared to untreated (Un) controls
Supplementary Table 4.2. Predicted gene targets of differentially expressed miRNAs in FhHDM-1 treated β-cells compared to untreated (Un) controls, common across all online miRNA gene target prediction tools mIRDB, DIANA and Target Scan
Supplementary Table 4.3A. List of predicted gene targets from miRNA upregulated in FhHDM-1 treated β-cells within each PANTHER DB category of molecular function and biological process (from Figure 2).
Supplementary Table 4.3B. KEGG pathway analysis of predicted gene targets from miRNA downregulated in FhHDM-1 treated β-cells compared to untreated controls
Supplementary Table 4.4. List of matched gene targets from miRNA downregulated in FhHDM-1 treated β-cells within each PANTHER DB category of molecular function and biological process (from Figure 4.5).
Supplementary Table 4.5. Differentially expressed miRNAs in FhHDM-1 treated β-cells exposed to pro-inflammatory cytokines, compared to cytokines alone
Supplementary Table 4.6. Predicted gene targets for differentially expressed miRNAs in FhHDM-1 treated β-cells exposed to pro-inflammatory cytokines compared to cytokines (CM) alone
Supplementary Table 4.7. Predicted gene targets of differentially expressed miRNAs in FhHDM-1 treated β-cells exposed to pro-inflammatory cytokines compared to cytokines (CM) alone, common across all online miRNA gene target prediction tools mIRDB, DIANA and Target Scan
Supplementary Table 4.8. KEGG pathway analysis of predicted gene targets from miRNA upregulated in FhHDM-1 treated β-cells exposed to pro-inflammatory cytokines compared to cytokines alone
Supplementary Table 4.9. KEGG pathway analysis of predicted gene targets from miRNA downregulated in FhHDM-1 treated β-cells exposed to pro-inflammatory cytokines compared to cyokines alone
Supplementary Table 4.10. Differentially expressed genes in the transcriptome of FhHDM-1 treated β-cells exposed to pro-inflammatory cytokines, compared to cytokines alone
Supplementary Table 4.11. Matched gene targets common between transcriptome and predicted gene targets of differentially expressed miRNA in FhHDM-1 treated β-cells under inflammatory conditions compared to pro-inflammatory cytokine only (CM) controls.
Supplementary Table 4.12. KEGG pathway analysis of matched genes downregulated in the transcriptome with their corresponding regulatory miRNA upregulated in FhHDM-1 β-cells exposed to pro-inflammatory cytokines compared to cytokines alone
Supplementary Table 4.13. KEGG pathway analysis of matched genes upregulated in the transcriptome with their corresponding regulatory miRNA downregulated in FhHDM-1 β-cells exposed to pro-inflammatory cytokines compared to cytokines alone