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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