2019_Swank_analysis

This repository contains data and code to accompany the article 'Cell-free gene regulatory network engineering with synthetic transcription factors' by Zoe Swank, Nadanai Laohakunakorn, and Sebastian J. Maerkl (https://doi.org/10.1101/407999). More information can be found in the paper or on our lab website. Notebooks may be viewed directly in GitHub or using the Jupyter nbviewer, which tends to work more reliably.

Requirements

All code was tested on python 3.6.4. We use numpy 1.13.3, scipy 1.0.0, and jupyter 1.0.0. MCMC fitting was carried out using emcee 2.2.1. Please see the requirements file for more information.

Notebooks

NB_bar_charts.ipynb generates bar charts for Figures 4 and 5A-B.

NB_models_thermo.ipynb defines and fits thermodynamic models to cooperative dose response curves, which are used to generate plots for Figure 5 and Supplementary Figure S4.

NB_models_Hill.ipynb defines and fits Hill function models to cooperative dose response curves, and generates Supplementary Figure S6.

NB_models_helix.ipynb defines and fits the helical promoter model, and generates plots for Figure 5.

NB_models_sens.ipynb determines the dose response sensitivity for cooperative repressors and generates Supplementary Figure S5.

NB_models_sitetuning.ipynb plots the results of MCMC sampling for the site tuning data, used to generate Supplementary Figure S4.

NB_TXTLdynamics.ipynb analyzes the dynamics of TXTL on-chip and on the plate reader, and generates Supplementary Figure S3.

helper.py contains a few useful functions which are required by the notebooks.

File structure

All notebooks and helper.py are contained in the top-level directory; additionally the notebooks require /data/, /plots/, and /output/ subdirectories from which to read data, and into which plots and MCMC sampling output files are written. Files written into the /output/ the output directory are ignored in this repository due to their large size but may be regenerated locally by running the notebooks.

Data

The /data/ directory contains the following files:

Cooperative dose response data:

2site_coop_PDZ.csv
2site_coop_GCN.csv
2site_coop_AAGCN.csv

Helical library data:

distance_chip_8A.csv

TXTL dynamics data from chip and plate reader:

dynamics_chip.csv
dynamics_PR.csv

Repressor characterization data on-chip:

repressor_1site_FR.csv
repressor_1site_KD.csv
repressor_1siteslide_KD.csv
repressor_1siteslidedwn_FR.csv
repressor_1siteslideup_FR.csv
repressor_2site_FR.csv
repressor_2site_KD.csv

Cooperative repressor characterization plate reader data:

repressor_platereader.csv

Output

All generated plots go to the /plots/ subfolder. MCMC samples go into the /output/ folder. These files may be very large.