Processed RNA-seq data associated with the manuscript by Gong et al., Frontiers in Microbiology, 2025

This dataset contains the processed RNA-seq data supporting the manuscript: "Gong et al., Frontiers in Microbiology (2025)." According to the sequencing company’s data retention policy, raw FASTQ files are stored for only 6 months and were deleted before the data deposition stage. Therefore, all processed data directly exported from the official RNA-seq analysis pipeline are provided. Included in this dataset: • raw gene count matrix (featureCounts output)• sample metadata (experimental groups and conditions)• differential expression tables for all comparisons• quality control summaries (mapping statistics, sequencing metrics) These processed data are sufficient to reproduce all major analyses presented in the manuscript, including normalization, differential expression analysis, PCA, and downstream interpretation. No restrictions apply to data reuse. Please contact the corresponding author for questions regarding the dataset.