Source data for "Quantitative profiling of millions of nucleotides reveals sequence-encoded interactions that govern plasmid propagation"

Source data for "Quantitative profiling of millions of nucleotides reveals sequence-encoded interactions that govern plasmid propagation" This dataset contains all processed experimental data underlying the figures and analyses reported in the manuscript. Files are organised into four folders: Single Part Assay — LFC fitness scores and sequence data for 192 MTK plasmids propagated in E. coli DH5α, DH10B and Stbl3, including concatemer percentage metrics, transcription factor binding site (TFBS) presence matrices (FIMO against DPInteract), and targeted long-read transcriptomics measurements. 4-Part Assembly Assay (rf training data) — LFC fitness scores and sequence data for 1,847 four-part combinatorial mammalian expression cassette assemblies, used to train the random forest part-identity model. Pairwise Ranking Ablation Study — Results of the mechanistic feature ablation analysis combining transcriptional output, concatemer load, and TFBS content as predictors of plasmid fitness. UNet Training Data — Processed LFC fitness scores for 124,339 degenerate 192 bp sequence variants used to train the TRACE U-Net convolutional neural network. All LFC values represent the log fold change in relative plasmid abundance over 16 hours of batch culture under antibiotic selection, measured by Oxford Nanopore or Illumina amplicon sequencing. Custom analysis code is available at https://github.com/tcopeman21/plasmid-host-interactions.