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Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging

Gabriele, Michele; Brandão, Hugo B.; Grosse-Holz, Simon; Jha, Asmita; Dailey, Gina M.; Cattoglio, Claudia; Hsieh, Tsung-Han S.; Mirny, Leonid; Zechner, Christoph; Hansen, Anders S.


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  <identifier identifierType="DOI">10.5281/zenodo.5770531</identifier>
  <creators>
    <creator>
      <creatorName>Gabriele, Michele</creatorName>
      <givenName>Michele</givenName>
      <familyName>Gabriele</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5393-9084</nameIdentifier>
      <affiliation>Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</affiliation>
    </creator>
    <creator>
      <creatorName>Brandão, Hugo B.</creatorName>
      <givenName>Hugo B.</givenName>
      <familyName>Brandão</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5496-0638</nameIdentifier>
      <affiliation>Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</affiliation>
    </creator>
    <creator>
      <creatorName>Grosse-Holz, Simon</creatorName>
      <givenName>Simon</givenName>
      <familyName>Grosse-Holz</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0717-5757</nameIdentifier>
      <affiliation>Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Jha, Asmita</creatorName>
      <givenName>Asmita</givenName>
      <familyName>Jha</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2612-551X</nameIdentifier>
      <affiliation>Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</affiliation>
    </creator>
    <creator>
      <creatorName>Dailey, Gina M.</creatorName>
      <givenName>Gina M.</givenName>
      <familyName>Dailey</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8988-963X</nameIdentifier>
      <affiliation>Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Cattoglio, Claudia</creatorName>
      <givenName>Claudia</givenName>
      <familyName>Cattoglio</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6100-0491</nameIdentifier>
      <affiliation>Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Hsieh, Tsung-Han S.</creatorName>
      <givenName>Tsung-Han S.</givenName>
      <familyName>Hsieh</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-2094-0772</nameIdentifier>
      <affiliation>Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Mirny, Leonid</creatorName>
      <givenName>Leonid</givenName>
      <familyName>Mirny</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0785-5410</nameIdentifier>
      <affiliation>Department of Physics and Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Zechner, Christoph</creatorName>
      <givenName>Christoph</givenName>
      <familyName>Zechner</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1300-6076</nameIdentifier>
      <affiliation>Max Planck Institute of Molecular Cell Biology &amp; Genetics; Dresden, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Hansen, Anders S.</creatorName>
      <givenName>Anders S.</givenName>
      <familyName>Hansen</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7540-7858</nameIdentifier>
      <affiliation>Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>Chromosome locus pair tracking</subject>
    <subject>CTCF depletion</subject>
    <subject>RAD21 depletion</subject>
    <subject>WAPL depletion</subject>
    <subject>Super-resolution live cell imaging</subject>
    <subject>Mouse embryonic stem cells</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-12-09</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5770531</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.5770530</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.0</version>
  <rightsList>
    <rights rightsURI="https://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;&lt;strong&gt;Overview&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;This repository contains all the raw and processed trajectory data associated with &amp;ldquo;paper title&amp;rdquo;. In this ReadMe file we provide the following information:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;The cell lines and conditions used in this study&lt;/li&gt;
	&lt;li&gt;A summary of how the data was collected&lt;/li&gt;
	&lt;li&gt;The structure of the chromosome locus tracking data&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;Cell lines and conditions&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;In total, the dataset covers 12 experimental conditions representing the following cell lines and treatment conditions:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;C36&lt;/li&gt;
	&lt;li&gt;C65&lt;/li&gt;
	&lt;li&gt;C27&lt;/li&gt;
	&lt;li&gt;CTCF-AID (untreated)&lt;/li&gt;
	&lt;li&gt;CTCF-AID (2 hours AID)&lt;/li&gt;
	&lt;li&gt;CTCF-AID (4 hours AID)&lt;/li&gt;
	&lt;li&gt;RAD21-AID (untreated)&lt;/li&gt;
	&lt;li&gt;RAD21-AID (2 hours AID)&lt;/li&gt;
	&lt;li&gt;RAD21-AID (4 hours AID)&lt;/li&gt;
	&lt;li&gt;WAPL-AID (untreated)&lt;/li&gt;
	&lt;li&gt;WAPL-AID (4 hours AID)&lt;/li&gt;
	&lt;li&gt;WAPL-AID (6 hours AID)&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Data and data processing&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Trajectories were obtained from 3D timeseries of mouse embryonic stem cell colonies in the conditions listed above using a LSM900 Airyscan 2 Zeiss microscope. For each movie we recorded 365 frames of 49.69 &amp;micro;m x 49.69 &amp;micro;m (584 x 584 pixels, pixel size: 0.085 &amp;micro;m by 0.085 &amp;micro;m), separated by an interval of 20 seconds for a total of just over 2 hours. 3D images were composed of 30 z-stacks separated by 0.25 &amp;micro;m, for a total height of 7.25 &amp;micro;m. Imaging was performed in two colors allowing the tracking of two arrays of fluorophores on Chromosome 18 near the &lt;em&gt;Fbn2&lt;/em&gt; gene. In all conditions, the fluorophore arrays were separated by 515 kb (except the C27 clone where separation was 10 kb).&lt;/p&gt;

&lt;p&gt;The 3D image time series were processed using ConnectTheDots: &lt;a href="https://github.com/ahansenlab/connect_the_dots"&gt;https://github.com/ahansenlab/connect_the_dots&lt;/a&gt; to obtain paired trajectories of chromosome loci over time. The trajectories have been corrected for chromatic shifts and aberrations.&lt;/p&gt;

&lt;p&gt;Data are provided in an &amp;ldquo;unfiltered&amp;rdquo; format (meaning that individual dot localizations were not quality control filtered) , or a filtered format (the same data set, but having undergone quality control). The filtered (quality controlled) trajectory data was used for all the quantitative analyses in the article &amp;ldquo;&amp;rdquo;.&lt;/p&gt;

&lt;p&gt;File names are formatted follows.&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Quality controlled data have the structure: {Clone_and_condition_name}.tagged_set.tsv&lt;/li&gt;
	&lt;li&gt;Unfiltered data have the structure: {Clone_and_condition_name}.unfiltered.tagged_set.tsv&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;For example, for RAD21-AID tagged clone, for imaging performed after two hours of protein degradation, the quality-controlled file name is: RAD21_2_hr.tagged_set.tsv. Please note that for all no-treatment conditions, we used &amp;ldquo;0 hours&amp;rdquo; as the tag. Thus, the RAD21 (untreated) becomes RAD21_0_hr.tagged_set.tsv.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Structure of Data&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The trajectory data are provided as tab-separated text files consisting of 10 columns. The column headers are:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;id: a unique dot pair index&lt;/li&gt;
	&lt;li&gt;t: the frame in which the dots were localized&lt;/li&gt;
	&lt;li&gt;x: x-coordinate of the dot in the EGFP channel (units in &amp;micro;m)&lt;/li&gt;
	&lt;li&gt;y: y-coordinate of the dot in the EGFP channel (units in &amp;micro;m)&lt;/li&gt;
	&lt;li&gt;z: z-coordinate of the dot in the EGFP channel (units in &amp;micro;m)&lt;/li&gt;
	&lt;li&gt;x2: x-coordinate of the dot in the mScarlet channel (units in &amp;micro;m)&lt;/li&gt;
	&lt;li&gt;y2: y-coordinate of the dot in the mScarlet channel (units in &amp;micro;m)&lt;/li&gt;
	&lt;li&gt;z2: z-coordinate of the dot in the mScarlet channel (units in &amp;micro;m)&lt;/li&gt;
	&lt;li&gt;dist: 3D distance between the dots across channels (units in &amp;micro;m)&lt;/li&gt;
	&lt;li&gt;movie_index: an identifier used to link the dot pair back to the raw image timeseries.&lt;/li&gt;
&lt;/ul&gt;</description>
    <description descriptionType="Other">MG, HBB, SGH contributed equally to this study.</description>
  </descriptions>
</resource>
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