Data and code for developmental expression dynamics and associations of trehalose-6-phosphate-related and carbon–nitrogen metabolism genes in soybean nodules

This deposit supports a secondary analysis of public soybean nodule transcriptomes. The primary dataset, NCBI GEO GSE289665, contains 27 samples spanning 2–10 weeks post inoculation, with three biological replicates per stage. A sensitivity analysis omits sample 3wpi_R3. A separate eight-sample nodule inoculation dataset, GSE247823, supplies condition-specific candidate expression evidence. The archive contains estimated gene counts, saved edgeR objects, normalized expression matrices, sample design tables, frozen candidate annotations, time-effect and correlation results, processing sensitivity results, external integer counts, figure source values, selected figures, historical scripts, portable script copies, environment records and checksum manifests. Original experimental data were generated by the investigators of the cited GEO studies; this work generated no new plants or sequencing libraries. The analysis examines TPS/TPP and putative SnRK1α candidates together with carbon–nitrogen metabolism candidates. It distinguishes correlations across stage means from correlations after subtraction of stage means. The associations are exploratory and do not demonstrate metabolite concentrations, kinase activity, causal regulation of nitrogen fixation, or independent replication of pairwise associations. Reproduction starts from estimated counts and frozen candidate annotations. Raw-read alignment, complete genome-wide candidate discovery and the exact original prepDE implementation are outside this archive's reproduction scope. Figure-generation code for Figure 2A, Figure 3, Figure 4 and Figure 5 was executed using archived inputs, with numerical source-table agreement checked. Saved-object normalization checks were previously run on the server. A complete R pipeline rerun in a fresh environment, including refitting the external edgeR model, has not been performed locally. See README.md and verification/ for the precise checks and limitations. The archive reuses data from GEO GSE289665 and GSE247823 and must be cited together with those source studies. Author-owned code is licensed under MIT and author-owned derived data and documentation under CC BY 4.0. Third-party materials retain their original rights.