Dataset Open Access

Supplementary File S2: Plasmids for independently tunable, low-noise gene expression

Silva, João P. N.; Lopes, Soraia Vidigal; Grilo, Diogo J.; Hensel, Zach

Supplementary File S2 README

2019-April-26

"Plasmids for independently tunable, low-noise gene expression" (Version 2)

João P. N. Silva, Soraia Vidigal Lopes, Diogo J. Grilo, Zach Hensel

This file describes the contents of the supplementary file for this manuscript. Python scripts were run in a Python 3 environment on OSX with various scientific python packages updated as of April 2019. With minor modifications for any similar environment it should be possible to generate Figures 1, 2, and 4 in the manuscript from these scripts and raw data.

Contents:

\dna sequences
    \pDG101.gb Annotated DNA sequence in genbank format of plasmid pDG101
    \pJS101.gb Annotated DNA sequence in genbank format of plasmid pJS101 (AddGene #118280)
    \pJS102.gb Annotated DNA sequence in genbank format of plasmid pJS102 (AddGene #118281)
    \pZH501.gb Annotated DNA sequence in genbank format of plasmid pZH501
    \pZH509.gb Annotated DNA sequence in genbank format of plasmid pZH509 (AddGene #102664)
    \pZH713.gb Annotated DNA sequence in genbank format of plasmid pZH713
    \ZHX99.gb Annotated DNA sequence in genbank format for E. coli MG1655 chromosome insertion mutant ZHX99
    
\data
    \DG FCS Data: Raw flow cytometry data from BioRad S3 sorted by day and experimental condition; file name format: plasmid_inducer-concentration_inducer-units_inducer.fcs
    \pJS101 pDG101 independence
        \"quick scope intensity.ijm" Fiji macro used to extract average fluorescence intensities
        \"Microscope Data\" Microscope data analyzed using the above Fiji macro; directory names indicate ATc and IPTG concentrations for each experimentation condition/replicate
        \"intensity analysis\"
            X_nM_ATc_Y_uM_IPTG.csv files: Exported CSV data from Fiji for each condition
            backgrounds.csv: Average intensity for every condition, image frame, and color for background subtraction
        \"images for Figure 4": Image stack with raw images used to generate Fig 4A and 4B

\code
    \fcsAnalysis_final_181228.py step-wise script for generating Figures 1 and 2 from FCS data
    \fcsCalcDirectory181228.py script containing functions for FCS analysis and figure generation
    \fcsImages PDF figures output by FCS analysis scripts
    \FlowCal-master Distribution of the FlowCal library used in analysis for this manuscript; this is distributed under the MIT license
    \scopeAnalysisWorkflow190430.py step-wise script for generating Figures 4C and 4D from cell fluorescence microscopy data in CSV format exported from Fiji
    \scopeCalcDirectory190430.py script containing functions for microscopy data analysis and figure generation

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