How does the rice transcriptome respond across early and later salt-alkali stress?
The analysis compared Na₂CO₃-treated and control Nipponbare rice at Day 1 and Day 5. Each condition contained three biological replicates, allowing the two treatment effects to be estimated separately rather than collapsing time into one contrast.
- Source dataset
- NCBI BioProject PRJNA895747
- Experimental design
- 4 groups × 3 biological replicates
- Input format
- Paired-end RNA-seq FASTQ plus sample metadata
- Reference
- Oryza sativa japonica IRGSP-1.0
Workflow and methods
The report records the toolchain, versions, statistical thresholds, and files passed between steps so the execution path can be inspected.
A larger strict response was detected at Day 5
Using the report’s strict threshold of FDR ≤ 0.01 and |log₂ fold change| ≥ 0.585, the analysis identified 1,451 differentially expressed genes at Day 1 and 2,005 at Day 5.
649 upregulated and 802 downregulated genes.
869 upregulated and 1,136 downregulated genes.
331 strict DEGs overlapped between timepoints.
1,120 genes were Day-1-specific and 1,674 were Day-5-specific.
Limitations and validation status
- The page reports computational results from this dataset; it does not claim independent experimental validation of individual genes.
- The session report exports enrichment-ready gene lists and ranked inputs, but it does not present interpreted GO or KEGG enrichment results. Those should not be implied as completed findings.
- The reported 331-gene overlap is based on the strict statistical threshold and should not be read as the complete biological response shared between timepoints.
- Software versions and thresholds reflect this recorded run and should be rechecked before reproducing the analysis in a different environment.
Reproduced by Pipette from public source data. Findings remain computational until supported by independent biological validation.
Reproducibility artifacts recorded in the session
The downloadable report lists the inputs, tools, versions, thresholds, output filenames, and generated figures. Representative artifacts include:
count_matrix.csv38,993 genes across 12 samplesde_results_day1/Complete Day 1 DESeq2 result setde_results_day5/Complete Day 5 DESeq2 result setoverlap_genes_strict.csv331 genes significant at both timepointsgsea_ranked_day1.csvRanked Day 1 genes for downstream analysissample_qc_table.csvRead depth, detection, and alignment metrics