Supplementary Tables Chapter 6 - Coco Duizer

Supplementary Tables Chapter 6 - Coco Duizer

Table S1. DEG HT29 ADP-heptose Flagellin.
Differentially expressed genes in HT-29 cells after stimulation with ADP-heptose or flagellin as calculated using DESeq2. Genes with a minimum fold-increase of 2 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction are shown. Upregulated genes are shown in green, downregulated genes are shown in red.

Table S2. Venn HT-29 ADP-heptose Flagellin.
Differentially expressed genes, as calculated in Table S1, that are uniquely upregulated in ADP-heptose-stimulated HT-29 cells (HT-29 ADP-heptose-up), uniquely upregulated in flagellin-stimulated HT-29 cells (HT-29 Flagellin-up), or upregulated in both ADP-heptose-, and flagellin-stimulated HT-29 cells (HT-29 ADP-heptose-up:HT-29 Flagellin-up).

Table S3. Table 3 - KEGG Enrichment HT-29 ADP-heptose Flagellin.
Upregulated pathways and genesets as calculated by KEGG over-representation analysis and KEGG gene set enrichtment analysis (GSEA) in HT-29 cells following stimulation with ADP-heptose or flagellin. Pathways and geneset with an adjusted p value of <0.05 are shown.

Table S4. DEG Organoids Flagellin.
Differentially expressed genes in rectal organoids after stimulation with flagellin as calculated using DESeq2. Genes with a minimum fold-increase of 2 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction are shown. Upregulated genes are shown in green, downregulated genes are shown in red.

Table S5. DEG PBMC ADP-heptose LPS.
Differentially expressed genes in PBMCs after stimulation with ADP-heptose or LPS as calculated using DESeq2. Genes with a minimum fold-increase of 1 and 2 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction are shown. Upregulated genes are shown in green, downregulated genes are shown in red.

Table S6. Venn PBMC ADP-heptose LPS.
Differentially expressed genes, as calculated in Table S5 in ADP-heptose- or LPS-stimulated PBMCs. The first tab shows differentially expressed genes that are uniquely upregulated in ADP-heptose-stimulated PBMCs (PBMC ADP-heptose-up), uniquely upregulated in LPS-stimulated PBMC (PBMC LPS-up), or upregulated in both ADP-heptose-, and LPS-stimulated PBMC (PBMC ADP-heptose-up:PBMC LPS-up). The second tab shows differentially expressed genes that are uniquely downregulated in ADP-heptose-stimulated PBMCs (PBMC ADP-heptose-down), uniquely downregulated in LPS-stimulated PBMCs (PBMC LPS-down), or downregulated in both ADP-heptose-, and LPS-stimulated PBMCs (PBMC ADP-heptose-down:PBMC LPS-down). Genes in the Venn diagram and this table had a minimum fold-increase of 1 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction.

Table S7. KEGG Enrichment PBMC ADP-heptose LPS.
Differentially regulated pathways and genesets as calculated by KEGG over-representation analysis and KEGG GSEA in PBMCs following stimulation with ADP-heptose or LPS. Pathways and geneset with an adjusted p value of <0.05 are shown.

Table S8. Venn HT-29 PBMC ADP-heptose.
Differentially expressed genes, as calculated in Tables S1 and S5, in ADP-heptose-stimulated HT-29 cells and PBMCs. The first tab shows differentially expressed genes that are uniquely upregulated in ADP-heptose-stimulated HT-29 cells (HT-29 ADP-heptose-up), uniquely upregulated in ADP-heptose-stimulated PBMC (PBMC ADP-heptose-up), or upregulated in both ADP-heptose-stimulated HT-29 cells and PBMCs (HT-29 ADP-heptose-up:PBMC ADP-heptose-up). The second tab shows differentially expressed genes that are uniquely downregulated in ADP-heptose-stimulated HT-29 cells (HT-29 ADP-heptose-down), uniquely downregulated in ADP-heptose-stimulated PBMC (PBMC ADP-heptose-down) or downregulated in both ADP-heptose-stimulated HT-29 cells and PBMCs (HT-29 ADP-heptose-down:PBMC ADP-heptose-down). Genes in the Venn diagram and this table had a minimum fold-increase of 2 (HT-29 cells) or 1 (PBMCs) with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction.

Table S9. KEGG Enrichment HT-29 PBMC ADP-heptose.
Differentially regulated pathways as calculated by KEGG over-representation analysis in HT-29 and PBMCs following stimulation with ADP-heptose. Pathways with an adjusted p value of <0.05 are shown.