Trained checkpoints and processed expression matrices for "Forward-drive dosage stratifies a coordinated regulatory state in logic-gated Salmonella"

This record contains the trained model checkpoints and processed gene-expression matrices supporting Yu, Ge & Cui, "Forward-drive dosage stratifies a coordinated regulatory state in logic-gated Salmonella" . Contents: (1) trained checkpoints for the graph-constrained, small-RNA-aware transcriptional model used in the study only as a measuring instrument (the conservative comparator in Figure 4); (2) processed per-library expression matrices (CPM) for the engineered Salmonella Typhimurium strains — SL7207 (parent), Δasd, YB1 (1× pepT-asd) and PW (2× pepT-asd) — profiled by Oxford Nanopore direct-RNA sequencing across aerobic and anaerobic conditions. Analysis and figure code: https://github.com/binyu8589-cpu/yb1-cross-species-simulator (MIT). Raw sequencing reads: NCBI GEO GSE333492. The metadata of this record previously referenced an earlier manuscript on model epistemic boundaries; the deposited files are unchanged.