Macrophage response specificity to ligand mixtures is improved by signaling pathway antagonism

This dataset accompanies the study "Macrophage response specificity to ligand mixtures is improved by signaling pathway antagonism." It contains single-cell NFκB signaling data for macrophages exposed to single immune ligands and to combinatorial (mixed) ligand stimuli, combining experimental measurements with mechanistic single-cell model simulations. Five ligands are studied—TNF, LPS, CpG, PolyIC (pIC), and Pam3CSK—acting through the TNFR, TLR4, TLR9, TLR3, and TLR1/2 receptor modules. Data span single ligands and all of their pairwise, triple, quadruple, and five-way combinations (31 combinatorial conditions), along with dose-response grids for each ligand pair used to map synergistic and antagonistic interaction regimes, including the proposed CpG/polyIC endosomal-transport competition mechanism and the CD14-dependent LPS/Pam3CSK interaction. Files are provided in MATLAB v5 (.mat) and CSV formats. Each dataset records single-cell nuclear NFκB activity trajectories (arbitrary units, 5-minute sampling over ~8 hours; ~97–98 time points per cell), six interpretable "signaling codons" derived from each trajectory (Duration, EarlyVsLate, OscVsNonOsc, PeakAmplitude, Speed, TotalActivity), and a comprehensive package of ~105 dynamic single-cell features (peak, oscillation, integral, derivative, timing, and signal-quality metrics). Simulation files additionally include the sampled model-parameter distributions and the molecular species saved per condition. Contents include: experimental single-cell datasets; pooled experimental-plus-simulated codon datasets; all-combination stimulus-response simulations and matched "no-competition" controls; per-ligand-pair dose-grid simulations; CD14-focused simulations; an unstimulated baseline; condition-to-condition response-distance matrices; and machine-learning-formatted feature matrices and labels for classifying stimulation condition from signaling codons. A companion DATA_README.txt documents every file, variable, and condition in detail.