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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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        "affiliation": "Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa", 
        "name": "Lopes, Soraia Vidigal", 
        "orcid": "0000-0002-3705-2619"
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        "affiliation": "Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa", 
        "name": "Grilo, Diogo J.", 
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        "affiliation": "Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa", 
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    "description": "<p>Supplementary File S2 README</p>\n\n<p>2018-Jan-09</p>\n\n<p>&quot;Plasmids for independently tunable, low- noise gene expression&quot;</p>\n\n<p>Jo\u00e3o P. N. Silva, Soraia Vidigal Lopes, Diogo J. Grilo, Zach Hensel</p>\n\n<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 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.</p>\n\n<p>Contents:</p>\n\n<p>\\dna sequences<br>\n&nbsp;&nbsp; &nbsp;\\pDG101.gb Annotated DNA sequence in genbank format of plasmid pDG101<br>\n&nbsp;&nbsp; &nbsp;\\pJS101.gb Annotated DNA sequence in genbank format of plasmid pJS101 (AddGene #118280)<br>\n&nbsp;&nbsp; &nbsp;\\pJS102.gb Annotated DNA sequence in genbank format of plasmid pJS102 (AddGene #118281)<br>\n&nbsp;&nbsp; &nbsp;\\pZH501.gb Annotated DNA sequence in genbank format of plasmid pZH501<br>\n&nbsp;&nbsp; &nbsp;\\pZH509.gb Annotated DNA sequence in genbank format of plasmid pZH509 (AddGene #102664)<br>\n&nbsp;&nbsp; &nbsp;\\pZH713.gb Annotated DNA sequence in genbank format of plasmid pZH713<br>\n&nbsp;&nbsp; &nbsp;\\ZHX99.gb Annotated DNA sequence in genbank format for E. coli MG1655 chromosome insertion mutant ZHX99<br>\n&nbsp;&nbsp; &nbsp;<br>\n\\data<br>\n&nbsp;&nbsp; &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<br>\n&nbsp;&nbsp; &nbsp;\\pJS101 pDG101 independence<br>\n&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;\\&quot;quick scope intensity.ijm&quot; Fiji macro used to extract average fluorescence intensities<br>\n&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;\\&quot;Microscope Data\\&quot; Microscope data analyzed using the above Fiji macro; directory names indicate ATc and IPTG concentrations for each experimentation condition<br>\n&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;\\&quot;intensity analysis\\&quot;<br>\n&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;X_nM_ATc_Y_uM_IPTG.csv files: Exported CSV data from Fiji for each condition<br>\n&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;backgrounds.csv: Average intensity for every condition, image frame, and color for background subtraction<br>\n&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;\\&quot;images for Figure 4&quot;: Image stack with raw images used to generate Fig 4A and 4B</p>\n\n<p>\\code<br>\n&nbsp;&nbsp; &nbsp;\\fcsAnalysis_final_181228.py step-wise script for generating Figures 1 and 2 from FCS data<br>\n&nbsp;&nbsp; &nbsp;\\fcsCalcDirectory181228.py script containing functions for FCS analysis and figure generation<br>\n&nbsp;&nbsp; &nbsp;\\fcsImages PDF figures output by FCS analysis scripts<br>\n&nbsp;&nbsp; &nbsp;\\FlowCal-master Distribution of the FlowCal library used in analysis for this manuscript<br>\n&nbsp;&nbsp; &nbsp;\\scopeAnalysisWorkflow190107.py step-wise script for generating Figures 4C from cell fluorescence microscopy data in CSV format exported from Fiji<br>\n&nbsp;&nbsp; &nbsp;\\scopeCalcDirectory190107.py script containing functions for microscopy data analysis and figure generation</p>", 
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