Additional file 1 of Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula
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- Knaack, Sara A.; Conde, Daniel; Chakraborty, Sanhita; Balmant, Kelly M.; Irving, Thomas B.; Maia, Lucas Gontijo Silva; Triozzi, Paolo M.; Dervinis, Christopher; Pereira, Wendell J.; Maeda, Junko; Schmidt, Henry W.; Ané, Jean-Michel; Kirst, Matias; Roy, Sushmita
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Additional file 1: Table S1. Primers used in the RNAi validation study. Figure S1. Analysis workflow. Figure S2. Detailed DE gene statistics summary. Figure S3. Supplementary ESCAROLE clustering results. Figure S4. ATAC-seq data alignment statistics and fragment length distributions. Figure S5. ATAC-seq activity heatmaps and line plots for ±1 kb TSS regions in LCO-treatment data. Figure S6. ATAC-seq activity heatmaps and line plots for ±1 kb TSS regions in the comparable Maher et al. Medicago root sample data. Figure S7. Correlation of aggregated ATAC-seq activity for ±2 kb promoter regions. Figure S8. Supplementary ATAC-seq promoter analysis plots. Figure S9. Supplementary ATAC-seq peak-calling analysis plots. Figure S10. DRMN hyper-parameter tuning summary. Figure S11. DRMN module network edge-weight summary. Figure S12. DRMN module GO enrichment summary. Figure S13. Summary of ESCAROLE and DRMN transitioning gene set statistics and comparison. Figure S14. Summary of MTG-LASSO results and parameter tuning. Figure S15. Supplementary RNAi validation information.