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README.md

README.md

DOI

An Allosteric Theory of Transcription Factor Induction

This repository contains all experimental data and programs for the analysis found in "An Allosteric Theory of Transcription Factor Induction" by Manuel Razo-Mejia*, Stephanie Barnes*, Nathan Belliveau*, Griffin Chure*, Tal Einav*, and Rob Phillips.

An index for the structure of this repository is given below.

code

This folder contains the hand-written Python programs for processing, analyzing, and displaying the data presented in this work.

  • analysis/ | Jupyter Notebooks containing Python code and explanation for the myriad analyses described in the main text and supplemental information.

  • examples/ | Example Python scripts used for processing and analysis of raw data as well as for generating the figures found in the main text and the supplemental information.

  • mwc_induction_utils.py | A Python file containing the homegrown functions used in all processing and analysis procedures.

data

This folder contains all experimental data used in the publication. All csv files obey the tidy data guidelines.

  • flow_master.csv | All experimentally measured fold-change values obtained through flow cytometry.

  • microscopy_master.csv | All experimentally measured fold-change values obtained through single-cell microscopy. Please see the supplemental information for a more detailed description.

  • Oid_microscopy_master.csv | All microscopy measurments of the Oid synthetic operator used in the Supplemental Information F.

  • tidy_lacI_titration_data.csv | The LacI repressor titration data from Garcia and Phillips 2011 and Brewster et al. 2014.

  • flow_cytometry_comments/ | All comments associated with the experimental runs shown in the flow_master.csv file.

  • microscopy_comments/ | All comments associated with the experimental runs shown in microscopy_master.csv and Oid_microscopy_master.csv.

  • mcmc_flatchains/ | All Markov Chain Monte Carlo sampler flatchains used for parameter estimation saved as .pkl files.

  • example_flow_csv/ | A collection of representative flow cytometry .csv files used for the example processing.py file.

other

This folder contains other various files used in the publication.

  • plasmid_maps/ | A collection of the plasmid sequences used in this work as GenBank (.gb) files.

  • materials_list.txt | A list of the materials used in this work along with their catalog numbers.