EcN_analysis

Files accompanying Triassi et al., Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden, Cell Systems (2023), https://doi.org/10.1016/j.cels.2023.05.004

There are four folders:

• dna-maps_genbank

  • genbank files for plasmids and genome integrations in this paper

• rna-seq

  • All codes utilized in producing RNA-seq-related data and plots can be found in: EcN_analysis.py
  • Metadata including experimental information can be found in: 2021_01_07_EcN_hdoost_h_dataframe.csv
  • Analyzed output differential expression and p-values are shown in: 2021_04_09_DE_all_23h.csv
  • Other .csv files include QC, metrics, and raw & FPKM values for gene expression.

• plotted_data_only

  • Excel files containing values used to generate plots, no data anaylsis

• raw-data_code_and_notebooks

  • a bunch of Python notebooks used to analyze raw data and generate plots
    • notebooks are nested within subfolders
    • notebooks often contain superfluous code from prototyping or copied from previous analysis, some thinking will be required to run these
    • some raw data files were too large to upload to GitHub, but files can be shared upon request
  • Python scripts that are utilized by these notebooks
    • cytoflow_modules
      • cf_helpers.py and cf_imports.py
    • transferfunction.py
      • defines a class for creating transfer functions
    • transferfunction_beta.py
      • updated version used in later notebooks