Analysis package for RNA sequencing of pea (Pisum sativum) seed germination under PEG-induced osmotic stress across five genotypes: reference transcriptome, functional annotation, differential expression and co-expression network results

This dataset provides the analysis-output package supporting RNA sequencing of germinating pea (Pisum sativum L.) seeds from five genotypes (JI92, Trendy, 05L0100251/L0251, ATC7025, Cameor) selected to represent contrasting germination-stage tolerance to polyethylene glycol (PEG)-induced osmotic stress. Seeds were sampled at three states (mature dry seed, water-imbibed control, 15% PEG6000-imbibed) with three biological replicates per genotype-by-state combination (45 RNA-seq libraries). The package contains: (1) a de novo reference transcriptome (33,286 non-redundant transcripts, built via HISAT2/StringTie genome-guided assembly and EviGene redundancy reduction against the Pisum sativum JIC_Psat_v1.3 genome assembly); (2) EnTAP/InterProScan functional annotation of the reference transcriptome (GO terms, COG categories, KEGG pathways, InterPro domains); (3) DESeq2 differential expression results for the PEG-vs-water contrast in each genotype, including per-genotype significant DEG lists and the core cross-genotype shared DEG set; (4) a weighted gene co-expression network analysis (WGCNA, 25 modules across all 45 samples) with module-trait correlations, hub-gene tables, Cytoscape network files, and combined per-module functional enrichment summaries. Raw paired-end sequencing reads and gene-level count/TPM matrices for the same 45 libraries are deposited separately at NCBI GEO/SRA under GEO Series GSE341491, BioProject PRJNA1502490 (45 BioSamples SAMN61978349-SAMN61978393, 45 SRA Runs SRR39842865-SRR39842909). This package is the companion analysis output described in the associated Data in Brief article.