Silva, João P. N.
Lopes, Soraia Vidigal
Grilo, Diogo J.
Hensel, Zach
2019-01-09
<p>Supplementary File S2 README</p>
<p>2019-April-26</p>
<p>"Plasmids for independently tunable, low-noise gene expression" (Version 2)</p>
<p>João P. N. Silva, Soraia Vidigal Lopes, Diogo J. Grilo, Zach Hensel</p>
<p>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.</p>
<p>Contents:</p>
<p>\dna sequences<br>
\pDG101.gb Annotated DNA sequence in genbank format of plasmid pDG101<br>
\pJS101.gb Annotated DNA sequence in genbank format of plasmid pJS101 (AddGene #118280)<br>
\pJS102.gb Annotated DNA sequence in genbank format of plasmid pJS102 (AddGene #118281)<br>
\pZH501.gb Annotated DNA sequence in genbank format of plasmid pZH501<br>
\pZH509.gb Annotated DNA sequence in genbank format of plasmid pZH509 (AddGene #102664)<br>
\pZH713.gb Annotated DNA sequence in genbank format of plasmid pZH713<br>
\ZHX99.gb Annotated DNA sequence in genbank format for E. coli MG1655 chromosome insertion mutant ZHX99<br>
<br>
\data<br>
\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<br>
\pJS101 pDG101 independence<br>
\"quick scope intensity.ijm" Fiji macro used to extract average fluorescence intensities<br>
\"Microscope Data\" Microscope data analyzed using the above Fiji macro; directory names indicate ATc and IPTG concentrations for each experimentation condition/replicate<br>
\"intensity analysis\"<br>
X_nM_ATc_Y_uM_IPTG.csv files: Exported CSV data from Fiji for each condition<br>
backgrounds.csv: Average intensity for every condition, image frame, and color for background subtraction<br>
\"images for Figure 4": Image stack with raw images used to generate Fig 4A and 4B</p>
<p>\code<br>
\fcsAnalysis_final_181228.py step-wise script for generating Figures 1 and 2 from FCS data<br>
\fcsCalcDirectory181228.py script containing functions for FCS analysis and figure generation<br>
\fcsImages PDF figures output by FCS analysis scripts<br>
\FlowCal-master Distribution of the FlowCal library used in analysis for this manuscript; this is distributed under the MIT license<br>
\scopeAnalysisWorkflow190430.py step-wise script for generating Figures 4C and 4D from cell fluorescence microscopy data in CSV format exported from Fiji<br>
\scopeCalcDirectory190430.py script containing functions for microscopy data analysis and figure generation</p>
https://doi.org/10.5281/zenodo.2671633
oai:zenodo.org:2671633
Zenodo
https://doi.org/10.5281/zenodo.2536104
info:eu-repo/semantics/openAccess
MIT License
https://opensource.org/licenses/MIT
Supplementary File S2: Plasmids for independently tunable, low-noise gene expression
info:eu-repo/semantics/other