Data and analysis scripts for:

Forcier et al. Measuring cis-regulatory energetics in living cells using allelic manifolds. bioRxiv doi:10.1101/380972 (2018)

Directory structure:

• code/: Python analysis scripts and Jupyter notebooks
• data/: Metadata, raw data, and processed data for this study
  • constructs/: DNA sequence constructs used in this study
  • literature/: Data extracted from the prior literature
  • plate_reader/: Raw data from plate reader used for Miller assays
  • glycerol_stocks.xlsx: List of glycerol stocks used in this study
• figures/: Computationally rendered components of the figures in the manuscript.
• manuscript/: Copy of Precision dissection of cis-regulatory energetics in living cells.
• preprocessing/: Code and intermediate files for processing raw data
  • data/: Processed data and metadata for this study
    • glycerol_stocks.xlsx: List of glycerol stocks used in this study
    • library_clusters.py: CRP-RNAP spacing library clustering by glycerol stock
    • plate_panel.pkl: Pandas panel of raw Miller assay data, organized by plate
    • seq_spacing.xlsx: Sequence and CRP-RNAP spacing information for glycerol stocks
  • intermediates/: Fits and resamplings of model to processed data
  • results.xlsx: Complete summary of processed data
  • scripts/: Python analysis scripts for preprocessing
    • 18.10.30_init_fits.py: Script for generating the fit of all data for c61, occlusion, and conjoined libraries
    • 18.10.30_param_exp_c61.py: Script for exploring the effects of initial parameter selection on fitted values for c61 library
    • 18.10.30_param_exp_conj.py: Script for exploring the effects of initial parameter selection on fitted values for global fit to all libraries
    • 18.10.30_param_exp_occlusion.py: Script for exploring the effects of initial parameter selection on fitted values for occlusion library
    • 18.10.30_resamp_beta.py: Script for resampling all libraries for \beta' values
    • 18.10.30_resamp_c61.py: Script for resampling the library with CRP at -61.5
    • 18.10.30_resamp_cAMP_dilution.py: Script for resampling the data taken with varying cAMP concentrations for c71 and occlusion libraries
    • 18.10.30_resamp_conj.py: Script for resampling the global fit to all libraries
    • 18.10.30_resamp_occlusion.py: Script for resampling the library of constructs with CRP binding occluding the RNAP binding site
    • 18.10.30_summary_gen.py: Script for consolidating all intermediate processed data into summaries and results.xlsx
    • plate_processor.py: Script for processing raw data and generating plate_panel.pkl
• protocols/: Primary protocols used in this study