DOI: 10.6084/m9.figshare.25547083.v1
title: Meta-Analysis of Public RNA Sequencing Data of Drought and Salt Stresses in Different Phenotypes of <i>Oryza sativa</i>

description: <br><b>Supplementary Table 1</b> - 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.<br><b>Supplementary Table 2</b> - 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.<br><b>Supplementary Table 3</b> - 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.<br><b>Supplementary Table 4</b> - 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.<br><b>Supplementary Table 5</b> - Lists of upregulated genes of <i>Oryza sativa</i> for each of the four categories. The data is categorized into: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible.<br><b>Supplementary Table 6</b> - Lists of downregulated genes of <i>Oryza sativa</i> for each of the four categories. The data is categorized into: (1) salt-resistant, (2) salt-susceptible, (3) drought-resistant, and (4) drought-susceptible.<br><b>Supplementary Table 7</b> - Information of <i>Arabidopsis thaliana</i> ortholog genes corresponding to each gene of <i>Oryza sativa</i>. 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.<br><b>Supplementary Table 8</b> - The results of enrichment analysis for the upregulated and downregulated genes of <i>Oryza sativa</i>. The data is categorized into five groups: (1) all combined DEGs, (2) salt-resistant, (3) salt-susceptible, (4) drought-resistant, and (5) drought-susceptible.<br><b>Supplementary Table 9</b> - 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.<br><b>Supplementary Table 10</b> - 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.<br><b>Supplementary Table 11</b> - Gene lists of <i>Oryza sativa</i> 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.<br><b>Supplementary Table 12</b> - Comparison of <i>Oryza sativa</i> orthologous genes with previous <i>Arabidopsis thaliana</i> meta-analysis results. This file lists genes compared with previous studies by converting <i>Oryza sativa</i> gene IDs identified in this study to the corresponding <i>Arabidopsis thaliana</i> gene IDs. Differentially expressed genes of <i>Oryza sativa</i> under salt or drought stress were compared with differentially expressed genes of <i>Arabidopsis thaliana</i> under abscisic acid (ABA), salt, or drought treatments.(a) Upregulated genes(b) Downregulated genes<b>Supplementary Table 13</b> - Diterpenoid-related genes identified by meta-analysis<br>This table presents a list of diterpenoid metabolism-related genes identified through meta-analysis, showing either upregulation or downregulation in response to stress.<br><b>Supplementary Figure 1 </b>- 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 <i>Oryza sativa</i> 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.<b>Supplementary Figure 2</b> - Enrichment analysis of individual DEGs in <i>Oryza sativa</i> under different stress conditions<br>Enrichment analysis results for differentially expressed genes (DEGs) identified in <i>Oryza sativa</i> 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.<br><b>Supplementary Figure 3 </b>- Comparison of DEGs between resistant and susceptible phenotypes in <i>Oryza sativa</i> under salt and drought stress<br>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 <i>Oryza sativa</i> phenotypes. Enrichment analysis results for each gene set are also presented, showing significantly enriched GO terms and their associated statistical values.<br><b>Supplementary Figure 4 </b>- Comparison of stress-responsive genes between <i>Oryza sativa</i> and <i>Arabidopsis thaliana</i><br>UpSet plots illustrating the overlap of commonly regulated genes between <i>Oryza sativa</i> and <i>Arabidopsis thaliana</i> under various stress conditions. The plots show upregulated and downregulated genes across different stress treatments and phenotypes in both plant species.<br>(a) Upregulated genes(b) Downregulated genes<br>