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

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


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    <subfield code="a">&lt;p&gt;Supplementary File S2 README&lt;/p&gt;

&lt;p&gt;2018-Jan-09&lt;/p&gt;

&lt;p&gt;&amp;quot;Plasmids for independently tunable, low- noise gene expression&amp;quot;&lt;/p&gt;

&lt;p&gt;João P. N. Silva, Soraia Vidigal Lopes, Diogo J. Grilo, Zach Hensel&lt;/p&gt;

&lt;p&gt;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 December 2018. 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.&lt;/p&gt;

&lt;p&gt;Contents:&lt;/p&gt;

&lt;p&gt;\dna sequences&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\pDG101.gb Annotated DNA sequence in genbank format of plasmid pDG101&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\pJS101.gb Annotated DNA sequence in genbank format of plasmid pJS101 (AddGene #118280)&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\pJS102.gb Annotated DNA sequence in genbank format of plasmid pJS102 (AddGene #118281)&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\pZH501.gb Annotated DNA sequence in genbank format of plasmid pZH501&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\pZH509.gb Annotated DNA sequence in genbank format of plasmid pZH509 (AddGene #102664)&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\pZH713.gb Annotated DNA sequence in genbank format of plasmid pZH713&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\ZHX99.gb Annotated DNA sequence in genbank format for E. coli MG1655 chromosome insertion mutant ZHX99&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;&lt;br&gt;
\data&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\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&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\pJS101 pDG101 independence&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;\&amp;quot;quick scope intensity.ijm&amp;quot; Fiji macro used to extract average fluorescence intensities&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;\&amp;quot;Microscope Data\&amp;quot; Microscope data analyzed using the above Fiji macro; directory names indicate ATc and IPTG concentrations for each experimentation condition&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;\&amp;quot;intensity analysis\&amp;quot;&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;X_nM_ATc_Y_uM_IPTG.csv files: Exported CSV data from Fiji for each condition&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;backgrounds.csv: Average intensity for every condition, image frame, and color for background subtraction&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp; &amp;nbsp;\&amp;quot;images for Figure 4&amp;quot;: Image stack with raw images used to generate Fig 4A and 4B&lt;/p&gt;

&lt;p&gt;\code&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\fcsAnalysis_final_181228.py step-wise script for generating Figures 1 and 2 from FCS data&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\fcsCalcDirectory181228.py script containing functions for FCS analysis and figure generation&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\fcsImages PDF figures output by FCS analysis scripts&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\FlowCal-master Distribution of the FlowCal library used in analysis for this manuscript&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\scopeAnalysisWorkflow190107.py step-wise script for generating Figures 4C from cell fluorescence microscopy data in CSV format exported from Fiji&lt;br&gt;
&amp;nbsp;&amp;nbsp; &amp;nbsp;\scopeCalcDirectory190107.py script containing functions for microscopy data analysis and figure generation&lt;/p&gt;</subfield>
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