Meta-Analysis of Public RNA Sequencing Data of Drought and Salt Stresses in Different Phenotypes of <i>Oryza sativa</i>

Supplementary Table S1 - Summary of Oryza sativa sample metadata utilized in the meta-analysis. Supplementary Table S2 - Detailed metadata for curated datasets used in the meta-analysis. This includes stress condition, subspecies, project ID, run accession ID, cultivar, phenotype, library layout, tissue description, type of treatment, treatment time, and sequencing instrument. Supplementary Table S3 - TPM data for gene expression under stress conditions. This file contains the transcripts per million (TPM) data, categorized into four groups based on stress type and phenotype: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible. Supplementary Table S4 - TN-ratio data for gene expression under stress conditions. This file contains the TN-ratio data, representing the ratio of gene expression between stress-treated (T) and non-treated (N) samples. The data is categorized into four groups based on stress type and phenotype: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible. Supplementary Table S5 - 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 data is categorized into four groups based on stress type and phenotype: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible. Supplementary Table S6 - Lists of upregulated genes of Oryza sativa for each of the four categories. The data is categorized into: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible. Supplementary Table S7 - Lists of downregulated genes of Oryza sativa for each of the four categories. The data is categorized into: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible. Supplementary Table S8 - Information of Arabidopsis thaliana ortholog genes corresponding to each gene of Oryza sativa. The data is categorized into four groups based on stress type and phenotype: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible. Supplementary Table S9 - Read count data, DESeq2 analysis results, and comparison with TN-score method for salt-resistant rice. This table contains three main components: (1) the raw read counts from 24 salt-treated and 24 untreated samples used for DESeq2 analysis, (2) the differentially expressed genes (DEGs) identified by DESeq2 at various false discovery rate (FDR) thresholds (0.05, 0.01, 0.005, and 0.001) with log₂ fold change ≥ 1, and (3) a comparative analysis between the 82 upregulated genes identified by DESeq2 (FDR < 0.05) and the 397 genes selected by the TN-score approach. Supplementary Table S10 - (a) Gene list comparing DEGs identified by TN-score and DESeq2 methods in salt-resistant rice. Enrichment analysis results for each gene set: (b) common to both methods, (c) specific to the DESeq2 method, and (d) specific to the TN-score method. Supplementary Table S11 - The results of enrichment analysis for the upregulated and downregulated genes of Oryza sativa. The data is categorized into five groups: (1) all combined DEGs, (2) salt-resistant, (3) salt-susceptible, (4) drought-resistant, and (5) drought-susceptible. Supplementary Table S12 - Top two GO terms from enrichment analyses of individual DEGs of Oryza sativa under different stress conditions and phenotypes. Supplementary Table S13 - Number of common and unique DEGs between resistant and susceptible cultivars under salt and drought stress. Supplementary Table S14 - Top enriched terms from enrichment analysis of individual DEG groups associated with phenotypic differences in salt and drought stress responses in Oryza sativa. Supplementary Table S15 - Gene lists based on phenotype-specific differentially expressed genes (DEGs) under salt and drought stress conditions. This file compares DEGs between stress-resistant and stress-susceptible phenotypes for both stress types. It includes: (a) Upregulated genes common to both resistant and susceptible phenotypes under salt stress, and specific to each phenotype.(b) Upregulated genes common to both resistant and susceptible phenotypes under drought stress, and specific to each phenotype.(c) Downregulated genes common to both resistant and susceptible phenotypes under salt stress, and specific to each phenotype.(d) Downregulated genes common to both resistant and susceptible phenotypes under drought stress, and specific to each phenotype. Supplementary Table S16 - Enrichment analysis results for phenotype-specific DEGs under salt and drought stress conditions. The data includes enriched terms for each gene set categorized by stress type (salt and drought) and phenotype (resistant and susceptible), divided into 12 sheets corresponding to the gene lists from Supplementary Table 9: (a)-(c): Upregulated genes under salt stress ((a) resistant, (b) susceptible, and (c) common)(d)-(f): Downregulated genes under salt stress ((d) resistant, (e) susceptible, and (f) common)(g)-(i): Upregulated genes under drought stress ((g) resistant, (h) susceptible, and (i) common)(j)-(l): Downregulated genes under drought stress ((j) resistant, (k) susceptible, and (l) common)Enrichment analysis was conducted using ShinyGO 0.77, with "GO Biological Process" set to the "Pathway database". However, since no hits were found in gene set (j), only in that case the "All available gene sets" setting was used. Supplementary Table S17 - Gene lists of Oryza sativa commonly or specifically upregulated or downregulated across different stress conditions and phenotypes. The table includes: (a) Upregulated genes in both resistant and susceptible phenotypes under both salt and drought stresses.(b) Downregulated genes in both resistant and susceptible phenotypes under both salt and drought stresses.Supplementary Table S18 - Oryza sativa genes that were specifically regulated in the resistant or susceptible phenotype under both salt and drought stress conditions. Supplementary Table S19 - Comparison of Oryza sativa orthologous genes with previous Arabidopsis thaliana meta-analysis results. This file lists genes compared with previous studies by converting Oryza sativa gene IDs identified in this study to the corresponding Arabidopsis thaliana gene IDs. Differentially expressed genes of Oryza sativa under salt or drought stress were compared with differentially expressed genes of Arabidopsis thaliana under abscisic acid (ABA), salt, or drought treatments. (a) Upregulated genes(b) Downregulated genesSupplementary Table S20 - Diterpenoid-related genes identified by meta-analysis This table presents a list of diterpenoid metabolism-related genes identified through meta-analysis, showing either upregulation or downregulation in response to stress. Supplementary Table S21 - Comparison of mapping rates between japonica and indica reference transcriptomes. This table shows the mapping rates of 110 indica samples when aligned to both reference transcriptomes. The columns include: Sample_ID (sample identifier), Indica_Reference_Mapping_Rate(%) (percentage of reads mapped to the indica reference), Japonica_Reference_Mapping_Rate(%) (percentage of reads mapped to the japonica reference), and Mapping_Rate_Ratio(Indica/Japonica)(%) (the ratio of indica to japonica mapping rates expressed as a percentage). The data demonstrates that 102 out of 110 indica samples showed higher mapping rates when aligned to the japonica reference, supporting our choice of the japonica reference for comprehensive gene annotation analysis. Supplementary Table S22 - Comparison of Differentially Expressed Gene (DEG) analysis results when some data were excluded. (a) Table showing DEG lists and their comparison when samples with low mapping rates were excluded versus when all samples were used. (b) Table showing DEG lists and their comparison when root samples were excluded versus when all samples were used. (c) Table showing enrichment analysis results for the common DEG list between analyses with root samples excluded and all samples used. (d) Table showing enrichment analysis results for the DEG list when all samples were used. Supplementary Figure S1 - Tissue distribution of Oryza sativa samples utilized in the meta-analysis. Visualization of the distribution of RNA-seq sample tissue counts from different projects of Oryza sativa. Supplementary Figure S2 - Distribution of TN scores for genes in Oryza sativa under different stress conditions Scatter plots showing the distribution of TN scores for genes under salt and drought stress conditions in resistant and susceptible Oryza sativa cultivars. The x-axis represents genes ordered by their TN scores, while the y-axis displays the TN score for each gene. Differentially expressed genes (DEGs) were selected based on abrupt changes in these scores. Supplementary Figure S3 - (a) Venn diagram showing the comparison of the number of DEGs identified by TN-score and DESeq2 methods in salt-resistant rice. Figures showing enrichment analysis results for each gene set: (b) common to both methods, (c) specific to the DESeq2 method, and (d) specific to the TN-score method. Supplementary Figure S4 - Enrichment analysis of individual DEGs in Oryza sativa under different stress conditions Enrichment analysis results for differentially expressed genes (DEGs) identified in Oryza sativa under salt and drought stress conditions for resistant and susceptible phenotypes. The figure presents significantly enriched GO terms and their associated statistical values for each DEG set. Supplementary Figure S5 - Enrichment analysis of the combined DEGs with similar expression patterns across phenotypes and stress conditions (a) All upregulated genes with at least one DEG (b) All downregulated genes with at least one DEG. Supplementary Figure S6 - Comparison of DEGs between resistant and susceptible phenotypes in Oryza sativa under salt and drought stress Venn diagrams illustrating the overlap or specificity of (a) upregulated genes under salt stress, (b) downregulated genes under salt stress, (c) upregulated genes under drought stress, and (d) downregulated genes under drought stress between resistant and susceptible Oryza sativa phenotypes. Enrichment analysis results for each gene set are also presented, showing significantly enriched GO terms and their associated statistical values. Supplementary Figure S7 - Comparison of stress-responsive genes between Oryza sativa and Arabidopsis thaliana UpSet plots illustrating the overlap of commonly regulated genes between Oryza sativa and Arabidopsis thaliana under various stress conditions. The plots show upregulated and downregulated genes across different stress treatments and phenotypes in both plant species. (a) Upregulated genes(b) Downregulated genesSupplementary Figure S8 - Comparison of DEG analysis results when some data were excluded. (a) Venn diagram comparing the number of genes identified when samples with low mapping rates were excluded versus when all samples were used. (b) Venn diagram visualizing the comparison of the number of genes when root samples were excluded versus when all samples were used. (c) Figure showing enrichment analysis results for the common DEG list between analyses with root samples excluded and all samples used. (d) Figure showing enrichment analysis results for the DEG list when all samples were used.