Dataset Open Access

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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{
  "description": "<p><strong>Overview</strong></p>\n\n<p>This repository contains all the raw and processed trajectory data associated with &ldquo;paper title&rdquo;. In this ReadMe file we provide the following information:</p>\n\n<ul>\n\t<li>The cell lines and conditions used in this study</li>\n\t<li>A summary of how the data was collected</li>\n\t<li>The structure of the chromosome locus tracking data</li>\n</ul>\n\n<p><strong>Cell lines and conditions</strong></p>\n\n<p>In total, the dataset covers 12 experimental conditions representing the following cell lines and treatment conditions:</p>\n\n<ul>\n\t<li>C36</li>\n\t<li>C65</li>\n\t<li>C27</li>\n\t<li>CTCF-AID (untreated)</li>\n\t<li>CTCF-AID (2 hours AID)</li>\n\t<li>CTCF-AID (4 hours AID)</li>\n\t<li>RAD21-AID (untreated)</li>\n\t<li>RAD21-AID (2 hours AID)</li>\n\t<li>RAD21-AID (4 hours AID)</li>\n\t<li>WAPL-AID (untreated)</li>\n\t<li>WAPL-AID (4 hours AID)</li>\n\t<li>WAPL-AID (6 hours AID)</li>\n</ul>\n\n<p>&nbsp;</p>\n\n<p><strong>Data and data processing</strong></p>\n\n<p>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 &micro;m x 49.69 &micro;m (584 x 584 pixels, pixel size: 0.085 &micro;m by 0.085 &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 &micro;m, for a total height of 7.25 &micro;m. Imaging was performed in two colors allowing the tracking of two arrays of fluorophores on Chromosome 18 near the <em>Fbn2</em> gene. In all conditions, the fluorophore arrays were separated by 515 kb (except the C27 clone where separation was 10 kb).</p>\n\n<p>The 3D image time series were processed using ConnectTheDots: <a href=\"https://github.com/ahansenlab/connect_the_dots\">https://github.com/ahansenlab/connect_the_dots</a> to obtain paired trajectories of chromosome loci over time. The trajectories have been corrected for chromatic shifts and aberrations.</p>\n\n<p>Data are provided in an &ldquo;unfiltered&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 &ldquo;&rdquo;.</p>\n\n<p>File names are formatted follows.</p>\n\n<ul>\n\t<li>Quality controlled data have the structure: {Clone_and_condition_name}.tagged_set.tsv</li>\n\t<li>Unfiltered data have the structure: {Clone_and_condition_name}.unfiltered.tagged_set.tsv</li>\n</ul>\n\n<p>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 &ldquo;0 hours&rdquo; as the tag. Thus, the RAD21 (untreated) becomes RAD21_0_hr.tagged_set.tsv.</p>\n\n<p>&nbsp;</p>\n\n<p><strong>Structure of Data</strong></p>\n\n<p>The trajectory data are provided as tab-separated text files consisting of 10 columns. The column headers are:</p>\n\n<ul>\n\t<li>id: a unique dot pair index</li>\n\t<li>t: the frame in which the dots were localized</li>\n\t<li>x: x-coordinate of the dot in the EGFP channel (units in &micro;m)</li>\n\t<li>y: y-coordinate of the dot in the EGFP channel (units in &micro;m)</li>\n\t<li>z: z-coordinate of the dot in the EGFP channel (units in &micro;m)</li>\n\t<li>x2: x-coordinate of the dot in the mScarlet channel (units in &micro;m)</li>\n\t<li>y2: y-coordinate of the dot in the mScarlet channel (units in &micro;m)</li>\n\t<li>z2: z-coordinate of the dot in the mScarlet channel (units in &micro;m)</li>\n\t<li>dist: 3D distance between the dots across channels (units in &micro;m)</li>\n\t<li>movie_index: an identifier used to link the dot pair back to the raw image timeseries.</li>\n</ul>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139", 
      "@id": "https://orcid.org/0000-0002-5393-9084", 
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      "name": "Gabriele, Michele"
    }, 
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      "affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139", 
      "@id": "https://orcid.org/0000-0001-5496-0638", 
      "@type": "Person", 
      "name": "Brand\u00e3o, Hugo B."
    }, 
    {
      "affiliation": "Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA", 
      "@id": "https://orcid.org/0000-0002-0717-5757", 
      "@type": "Person", 
      "name": "Grosse-Holz, Simon"
    }, 
    {
      "affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139", 
      "@id": "https://orcid.org/0000-0002-2612-551X", 
      "@type": "Person", 
      "name": "Jha, Asmita"
    }, 
    {
      "affiliation": "Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA", 
      "@id": "https://orcid.org/0000-0002-8988-963X", 
      "@type": "Person", 
      "name": "Dailey, Gina M."
    }, 
    {
      "affiliation": "Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA", 
      "@id": "https://orcid.org/0000-0001-6100-0491", 
      "@type": "Person", 
      "name": "Cattoglio, Claudia"
    }, 
    {
      "affiliation": "Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA", 
      "@id": "https://orcid.org/0000-0003-2094-0772", 
      "@type": "Person", 
      "name": "Hsieh, Tsung-Han S."
    }, 
    {
      "affiliation": "Department of Physics and Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA", 
      "@id": "https://orcid.org/0000-0002-0785-5410", 
      "@type": "Person", 
      "name": "Mirny, Leonid"
    }, 
    {
      "affiliation": "Max Planck Institute of Molecular Cell Biology & Genetics; Dresden, Germany", 
      "@id": "https://orcid.org/0000-0003-1300-6076", 
      "@type": "Person", 
      "name": "Zechner, Christoph"
    }, 
    {
      "affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139", 
      "@id": "https://orcid.org/0000-0001-7540-7858", 
      "@type": "Person", 
      "name": "Hansen, Anders S."
    }
  ], 
  "url": "https://zenodo.org/record/5770531", 
  "datePublished": "2021-12-09", 
  "version": "1.0", 
  "keywords": [
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    "CTCF depletion", 
    "RAD21 depletion", 
    "WAPL depletion", 
    "Super-resolution live cell imaging", 
    "Mouse embryonic stem cells"
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  "@id": "https://doi.org/10.5281/zenodo.5770531", 
  "@type": "Dataset", 
  "name": "Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging"
}
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Publication date:
December 9, 2021
DOI:
10.5281/zenodo.5770531

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Keyword(s):
Chromosome locus pair tracking CTCF depletion RAD21 depletion WAPL depletion Super-resolution live cell imaging Mouse embryonic stem cells
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