Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses in <i>Arabidopsis thaliana</i>

Supplementary Table 1 - Metadata for curated datasets This file contains the metadata for the curated datasets used in the meta-analysis, including Sequence Read Archive (SRA) study ID, run ID, sample tissue, treatment type, treatment time, and sequence library type. Supplementary Table 2 - TPM data for gene expression under stress conditions This file contains the transcripts per million (TPM) data, five different treatment types (ABA, Salt, Dehydration, Mannitol, and Cold). Supplementary Table 3 - TN-ratio data for gene expression under stress conditions This file contains the TN-ratio data, which represents the ratio of gene expression between stress-treated (T) and non-treated (N) samples. Supplementary Table 4 - TN-score data for gene expression under stress conditions This file contains the TN-score data, calculated by subtracting the number of downregulated experiments from the number of upregulated experiments. The TN-score was used to assess changes in gene expression under stress conditions across experiments. Supplementary Table 5 - Read count data This file contains the read count data in ABA treatment and control samples. Supplementary Table 6 - The result of DESeq2 analysis in ABA treatment samples This file contains the result of Deseq2 analysis in ABA treatment samples. Significant changes are defined as 2-fold change, under multiple FDR thresholds (padj < 0.05, 0.01, 0.005, 0.001). Supplementary Table 7 - Lists of upregulated genes for each of the five stress treatment types This file contains the lists of upregulated genes identified in the Meta-analysis for each of the five stress treatment types. Supplementary Table 8 - Lists of downregulated genes for each of the five stress treatment types This file contains the lists of downregulated genes identified in the Meta-analysis for each of the five stress treatment types. Supplementary Table 9 - The lists and the result of enrichment analysis for the genes suggested to be upregulated by DESeq2 analysis This file contains the lists and the result of enrichment analysis for upregulated genes identified by DESeq2 in ABA treatment samples. Supplementary Table 10 - Overlap of commonly regulated genes across ABA, salt, and dehydration treatments This file contains the lists of commonly regulated genes across three stress treatments: ABA, Salt, and Dehydration. Supplementary Table 11 - The results of enrichment analysis for commonly regulated genes across ABA, salt, and dehydration treatments This file contains the results of the enrichment analysis focusing on 166 upregulated and 66 downregulated genes that are commonly regulated across three different stress treatments: ABA, Salt, and Dehydration. Supplementary Table 12 - Overlap of commonly upregulated genes across ABA, Salt, Dehydration, Mannitol, and Cold treatments This file contains the lists of commonly upregulated genes across five stress treatments: ABA, Salt, Dehydration, Mannitol, and Cold. Supplementary Table 13 - Overlap of Commonly Downregulated Genes across ABA, Salt, Dehydration, Mannitol, and Cold treatments This file contains the lists of commonly downregulated genes across five stress treatments: ABA, Salt, Dehydration, Mannitol, and Cold. Supplementary Table 14 - Overlap of commonly upregulated genes across ABA, Salt, Dehydration, Mannitol, Cold, and Hypoxia treatments This file contains the lists of commonly upregulated genes across six stress treatments: ABA, Salt, Dehydration, Mannitol, Cold, and Hypoxia. Supplementary Table 15 - Overlap of commonly downregulated genes across ABA, Salt, Dehydration, Mannitol, Cold, and Hypoxia treatments This file contains the lists of commonly downregulated genes across six stress treatments: ABA, Salt, Dehydration, Mannitol, Cold, and Hypoxia. Supplementary Figure 1 - Overlap of differentially expressed genes in TN-method and DESeq2 UpSet plots in (A-D) compare the overlap of genes selected by DESeq2 analysis and the TN-score method. In (A-D), the results are shown with different false discovery rate (FDR) thresholds for DESeq2. (A) Threshold FDR<0.05, upregulated genes (B) Threshold FDR<0.001, upregulated genes (C) Threshold FDR<0.05, downregulated genes (D) Threshold FDR<0.001, downregulated genes Supplementary Figure 2 - Enrichment analysis of differentially expressed genes for five stress treatment types Gene set enrichment analysis of the genes regulated under the five treatments is shown in (A–J), indicating upregulated and downregulated genes in the ABA (A, B), salt (C, D), dehydration (E, F), mannitol (G, H), and cold (I, J) treatments, respectively. Supplementary Figure 3 - Enrichment analysis of differentially expressed genes detected by DESeq2 This figure presents the results of enrichment analyses conducted on genes identified as upregulated by DESeq2 analysis. The analyses were performed at two different False Discovery Rate (FDR) thresholds: (A) FDR < 0.05, upregulated genes, 1144genes (B) FDR < 0.001, upregulated genes, 1018genes (C) FDR < 0.05, upregulated genes excluding TN2 selected genes, 676genes (D) FDR < 0.001, upregulated genes excluding TN2 selected genes, 554genes