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.第6章补充表格——Coco Duizer 表S1：HT-29细胞ADP-庚糖、鞭毛蛋白刺激差异表达基因。采用DESeq2分析经ADP-庚糖或鞭毛蛋白刺激后的HT-29细胞，筛选其中的差异表达基因。筛选标准为最小折叠变化≥2，经Benjamini-Hochberg校正后的错误发现率（FDR）为0.05。上调基因以绿色标注，下调基因以红色标注。 表S2：HT-29细胞ADP-庚糖、鞭毛蛋白刺激韦恩图。即表S1中计算得到的差异表达基因，分为三类：仅在ADP-庚糖刺激的HT-29细胞中上调的基因（HT-29 ADP-庚糖-上调）、仅在鞭毛蛋白刺激的HT-29细胞中上调的基因（HT-29 鞭毛蛋白-上调），以及在ADP-庚糖与鞭毛蛋白共同刺激的HT-29细胞中均上调的基因（HT-29 ADP-庚糖-上调:HT-29 鞭毛蛋白-上调）。 表S3：HT-29细胞ADP-庚糖、鞭毛蛋白刺激KEGG（京都基因与基因组百科全书）富集分析（正表格3）。采用KEGG过度表达分析与KEGG基因集富集分析（GSEA），计算经ADP-庚糖或鞭毛蛋白刺激后的HT-29细胞中上调的通路与基因集。筛选标准为校正后P值<0.05。 表S4：鞭毛蛋白刺激直肠类器官差异表达基因。采用DESeq2分析经鞭毛蛋白刺激后的直肠类器官，筛选其中的差异表达基因。筛选标准为最小折叠变化≥2，经Benjamini-Hochberg校正后的错误发现率为0.05。上调基因以绿色标注，下调基因以红色标注。 表S5：PBMC（外周血单个核细胞） ADP-庚糖、LPS（脂多糖）刺激差异表达基因。采用DESeq2分析经ADP-庚糖或脂多糖刺激后的外周血单个核细胞，筛选其中的差异表达基因。筛选标准为最小折叠变化分别为1和2，经Benjamini-Hochberg校正后的错误发现率为0.05。上调基因以绿色标注，下调基因以红色标注。 表S6：PBMC ADP-庚糖、LPS刺激韦恩图。即表S5中计算得到的、经ADP-庚糖或脂多糖刺激的外周血单个核细胞的差异表达基因。第一分页展示三类上调基因：仅在ADP-庚糖刺激的外周血单个核细胞中上调的基因（PBMC ADP-庚糖-上调）、仅在脂多糖刺激的外周血单个核细胞中上调的基因（PBMC LPS-上调），以及在ADP-庚糖与脂多糖共同刺激的外周血单个核细胞中均上调的基因（PBMC ADP-庚糖-上调:PBMC LPS-上调）。第二分页展示三类下调基因：仅在ADP-庚糖刺激的外周血单个核细胞中下调的基因（PBMC ADP-庚糖-下调）、仅在脂多糖刺激的外周血单个核细胞中下调的基因（PBMC LPS-下调），以及在ADP-庚糖与脂多糖共同刺激的外周血单个核细胞中均下调的基因（PBMC ADP-庚糖-下调:PBMC LPS-下调）。韦恩图及本表中的基因筛选标准为：经Benjamini-Hochberg校正后的错误发现率为0.05，最小折叠变化≥1。 表S7：PBMC ADP-庚糖、LPS刺激KEGG富集分析。采用KEGG过度表达分析与GSEA，计算经ADP-庚糖或脂多糖刺激后的外周血单个核细胞中差异调控的通路与基因集。筛选标准为校正后P值<0.05。 表S8：HT-29细胞、PBMC ADP-庚糖刺激韦恩图。即表S1与表S5中计算得到的、经ADP-庚糖刺激的HT-29细胞与外周血单个核细胞的差异表达基因。第一分页展示三类上调基因：仅在ADP-庚糖刺激的HT-29细胞中上调的基因（HT-29 ADP-庚糖-上调）、仅在ADP-庚糖刺激的外周血单个核细胞中上调的基因（PBMC ADP-庚糖-上调），以及在ADP-庚糖刺激的HT-29细胞与外周血单个核细胞中均上调的基因（HT-29 ADP-庚糖-上调:PBMC ADP-庚糖-上调）。第二分页展示三类下调基因：仅在ADP-庚糖刺激的HT-29细胞中下调的基因（HT-29 ADP-庚糖-下调）、仅在ADP-庚糖刺激的外周血单个核细胞中下调的基因（PBMC ADP-庚糖-下调），以及在ADP-庚糖刺激的HT-29细胞与外周血单个核细胞中均下调的基因（HT-29 ADP-庚糖-下调:PBMC ADP-庚糖-下调）。韦恩图及本表中的基因筛选标准为：HT-29细胞的最小折叠变化≥2，外周血单个核细胞的最小折叠变化≥1，且经Benjamini-Hochberg校正后的错误发现率为0.05。 表S9：HT-29细胞、PBMC ADP-庚糖刺激KEGG富集分析。采用KEGG过度表达分析，计算经ADP-庚糖刺激后的HT-29细胞与外周血单个核细胞中差异调控的通路。筛选标准为校正后P值<0.05。