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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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  <identifier identifierType="DOI">10.5281/zenodo.2536105</identifier>
  <creators>
    <creator>
      <creatorName>Silva, João P. N.</creatorName>
      <givenName>João P. N.</givenName>
      <familyName>Silva</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-4455-4286</nameIdentifier>
      <affiliation>Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa</affiliation>
    </creator>
    <creator>
      <creatorName>Lopes, Soraia Vidigal</creatorName>
      <givenName>Soraia Vidigal</givenName>
      <familyName>Lopes</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-3705-2619</nameIdentifier>
      <affiliation>Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa</affiliation>
    </creator>
    <creator>
      <creatorName>Grilo, Diogo J.</creatorName>
      <givenName>Diogo J.</givenName>
      <familyName>Grilo</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1279-3629</nameIdentifier>
      <affiliation>Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa</affiliation>
    </creator>
    <creator>
      <creatorName>Hensel, Zach</creatorName>
      <givenName>Zach</givenName>
      <familyName>Hensel</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4348-6229</nameIdentifier>
      <affiliation>Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Supplementary File S2: Plasmids for independently tunable, low- noise gene expression</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <dates>
    <date dateType="Issued">2019-01-09</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/2536105</alternateIdentifier>
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    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
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  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
  </descriptions>
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