RNA seq data for the article "Transcriptome reveals the mechanisms of nicotinamide regulating salt alkaline tolerance in soybeans"

The raw offline data was subjected to quality filtering using FASTP software (removing adapters, low-quality reads, and sequences with excessive N bases) to obtain high-quality clean reads. The clean reads were compared to the soybean reference genome using HISAT2 software (version information can be found in the comments), and gene expression levels were quantified using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.

Differential expression genes (DEGs) screening was based on DESeq2 (v1.38.3) software, with a threshold of | log ₂ FC |>1 and a corrected p-value (padj)<0.05. A total of 43727 genes were detected. At the same time, edgeR software was used to mine differentially expressed genes in six comparison groups: SA1 vs. CK, SA2 vs. CK, SA3 vs. CK, SA2 vs. SA1, SA3 vs. SA1, and SA3 vs. SA2, with the same threshold as above.

Enrichment analysis was completed using the clusterProfiler R package. Principal component analysis (PCA), Pearson correlation heatmap between samples, gene expression distribution density curve, and genome comparison statistics jointly verified the high repeatability and data quality of the samples.Along with transcriptome analysis, this study simultaneously measured the activity of antioxidant enzymes (POD, SOD, CAT, APX), ion content (Na ⁺, K ⁺), hydrogen peroxide (H ₂ O ₂) and superoxide anion (O ₂⁻ ·) content, photosynthetic pigments (chlorophyll a, chlorophyll b, carotenoids), osmoregulatory substances (soluble proteins, soluble sugars, proline), and levels of nicotinamide nucleotides (NAD ⁺, NADH, NADP ⁺, NADPH) in leaves.

All physiological indicators were detected using UV visible spectrophotometer or flame photometer, with three technical replicates set for each sample and expressed as mean ± standard deviation (SD).This dataset contains the following files: (1) Counts Matrix and FPKM/TPM Normalized Expression Matrix (in. txt format) for all samples; (2) Complete list of differentially expressed genes for each comparison group (in. xlsx format), including gene ID, log ₂ FC, P-value, and padj value; (3) QC reports and comparative statistical summary table; (4) GO and KEGG enrichment analysis results table; (5) RT qPCR validation of primer sequences and relative expression level data; (6) The raw measurement data of all physiological and biochemical indicators.

The data files are in common formats (. txt,. xlsx,. csv) and can be opened and processed using mainstream software such as Microsoft Excel, R software (v4.0 and above), and GraphPad Prism 9.0. There are no missing sequencing data, and all samples have passed quality control and successfully aligned to the reference genome. There is no systematic missing physiological indicator data, and the standard deviation range of some indicators has been indicated in the corresponding table.