Additional file 1: Table E1. RNA-Seq Quality Control Metrics. Table E2. Gene set enrichment analysis results corresponding to the CEBPD siRNA versus NT siRNA comparisons. Table E3. Gene set enrichment analysis results corresponding to the TNFα versus control comparisons. Table E4. Gene set enrichment analysis results corresponding to budesonide exposure. Table E5. Ontological categories enriched within gene co-expression groups. Table E6. RNA-Seq differential expression results for IL6R, SOCS3, SOCS1, and SOCS2 across the 10 comparisons made. Figure E1. Sample quality control prior to RNA-Seq via RT-qPCR of CEBPD and CXCL8. Figure E2. RNA-Seq data quality control. Figure E3. Significant gene set enrichment analysis categories corresponding to the CEBPD siRNA versus NT siRNA comparisons. Figure E4. Overall RNA-Seq results for each exposure were generally consistent with CEBPD knockdown. Figure E5. Significant gene set enrichment analysis categories corresponding to the TNFα versus control comparisons. Figure E6. TNFα-responsive genes whose expression changed with CEBPD knockdown selected from two significantly changed ontological categories. Figure E7. Significant gene set enrichment analysis categories corresponding to budesonide-responsive genes. Figure E8. Selection of soft-thresholding power (β) for weighted gene co-expression network analysis. Figure E9. Correlations between gene co-expression groups and phenotypes. Figure E10. CEBPD-binding sites near select IL-6 signaling pathway genes. Figure E11. Full representative immunoblots and CEBPD/Tubulin expression levels showing adequacy of CEBPD knockdown.
