Additional file 1 of Transcriptomic and physiological analyses of rice seedlings under different nitrogen supplies provide insight into the regulation involved in axillary bud outgrowth

Additional file 1: Table S1. The statistics of reads count of the RNA-seq data. Table S2. The primers used in our study. Table S3. The expression levels of all expressed genes and DEGs. Figure S1. Expression correlation between samples of RNA-seq. (a) Principal component analysis (PCA) shows tissue and N concentration specific samples (with repetition). Ab stands for axillary bud, Bp stands for basal part. (b) Expression correlations between two samples reveals the difference between axillary bud and basal part, and between different N concentrations. _1 and _2 stands for two repetitions. Figure S2. Specific and common genes between basal part and axillary bud under low N and high N conditions. (a) Venn diagram showing the overlaps among responsive genes in basal part and axillary bud under low and high N conditions. (b) The number of total and specific DEGs and TF genes in the four datasets shown in (a). (c) The common gene numbers between axillary bud and basal part under low N and high N conditions. Figure S3. Enriched GO terms within the category of cellular component (a) and molecular function (b) for DEGs in the ten expression patterns (B01-B09) in Fig. 4b. Only significant go terms (false discovery rate (FDR) < 0.05) are displayed. Figure S4. Enriched GO terms within the category of cellular component (a) and molecular function (b) for DEGs in the nine expression patterns (A01-A10) in Fig. 5b. Only significant go terms (false discovery rate (FDR) < 0.05) are displayed. Figure S5. Differentially expressed genes between basal part and axillary bud under each N concentration. (a) The number of up and down-regulated DEGs (fold change> 2 and padj< 0.05 by DESeq2) detected in axillary bud compared with basal part under six N concentrations. The number of up-, down- regulated and total DEGs for each N concentrations are shown. (b) Clustering the total DEGs detected between axillary bud and basal part under six N concentrations. FPKM values were scaled per gene across basal part samples and shown as the scaled expression. (c) Enriched GO terms within the category of biological process for the thirteen clusters shown in (b). Only significant go terms (false discovery rate (FDR) < 0.05) are displayed. Figure S6. Enriched GO terms within the category of cellular component (a) and molecular function (b) for DEGs in the thirteen expression patterns (BA01-BA13) in Additional file 1: Figure S5b. Only significant go terms (false discovery rate (FDR) < 0.05) are displayed. Figure S7. Overlap and specific genes between basal part and axillary bud under each N concentration. (a) Venn diagram analysis of Overlap and specific genes between basal part and axillary bud under each N concentration. (b) Enriched GO terms within the category of biological process for the overlap and specific genes (a). Only significant go terms (false discovery rate (FDR) < 0.05) are displayed. Figure S8. Differentially expressed TF genes in basal part (a) and axilary bud (b) under different N conditions. LN stands for low nitrogen, NN stands for normal nitrogen, HN stands for high nitrogen. B01-B09 and A01-A10 represent the clusters of DEGs in basal part (a) and axilary bud (b). Heatmaps show the expression patterns using scaled FPKM values. TF genes with FPKM values less than 1 in all 12 samples were not shown. Figure S9. Expression dynamics of TF families. Heatmaps show the expression patterns of TF families using scaled FPKM value of total TF genes in each family. Figure S10. Expression profiles of genes associated with ABA (a), GA (b), ethylene (c), and JA (d) in basal part and axillary bud under N concentrations. Heatmaps show the expression patterns using scaled FPKM values. Genes with FPKM values less than 1 in all samples were not shown. Figure S11. Expression profiles of genes associated with potassium transporters (a), phosphate transporters (b) and signaling (c) in basal part and axillary bud under different N concentrations. Genes with FPKM values less than 1 in all samples are not shown.