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.
MARC21 XML Export
<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
<leader>00000nmm##2200000uu#4500</leader>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">Chromosome locus pair tracking</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">CTCF depletion</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">RAD21 depletion</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">WAPL depletion</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">Super-resolution live cell imaging</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">Mouse embryonic stem cells</subfield>
</datafield>
<controlfield tag="005">20211210014845.0</controlfield>
<datafield tag="500" ind1=" " ind2=" ">
<subfield code="a">MG, HBB, SGH contributed equally to this study.</subfield>
</datafield>
<controlfield tag="001">5770531</controlfield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</subfield>
<subfield code="0">(orcid)0000-0001-5496-0638</subfield>
<subfield code="a">Brandão, Hugo B.</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA</subfield>
<subfield code="0">(orcid)0000-0002-0717-5757</subfield>
<subfield code="a">Grosse-Holz, Simon</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</subfield>
<subfield code="0">(orcid)0000-0002-2612-551X</subfield>
<subfield code="a">Jha, Asmita</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA</subfield>
<subfield code="0">(orcid)0000-0002-8988-963X</subfield>
<subfield code="a">Dailey, Gina M.</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA</subfield>
<subfield code="0">(orcid)0000-0001-6100-0491</subfield>
<subfield code="a">Cattoglio, Claudia</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA</subfield>
<subfield code="0">(orcid)0000-0003-2094-0772</subfield>
<subfield code="a">Hsieh, Tsung-Han S.</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Physics and Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA</subfield>
<subfield code="0">(orcid)0000-0002-0785-5410</subfield>
<subfield code="a">Mirny, Leonid</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Max Planck Institute of Molecular Cell Biology & Genetics; Dresden, Germany</subfield>
<subfield code="0">(orcid)0000-0003-1300-6076</subfield>
<subfield code="a">Zechner, Christoph</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</subfield>
<subfield code="0">(orcid)0000-0001-7540-7858</subfield>
<subfield code="a">Hansen, Anders S.</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">3615980</subfield>
<subfield code="z">md5:69339440363357be7beda98611cf4ac4</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/C27.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">5358430</subfield>
<subfield code="z">md5:6fd8c436d0b6411d406520738a981027</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/C27.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">5192863</subfield>
<subfield code="z">md5:5b45eee20c1a4c6c3c7a07caa4bd13f6</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/C36.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">7906793</subfield>
<subfield code="z">md5:834d0b996a5ea633e586c6bb4f538f1d</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/C36.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1519038</subfield>
<subfield code="z">md5:f2fc3e9ffbdf8e82639f58b65eb6a615</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/C65.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">2129493</subfield>
<subfield code="z">md5:7d8597533cd513bae8db2618214b0950</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/C65.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1301164</subfield>
<subfield code="z">md5:0b5baa2fbb5c4753ea7bafdf02c6e773</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/CTCF_0_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1970691</subfield>
<subfield code="z">md5:e334a17ec1c17393fd7d98e4e0df23a2</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/CTCF_0_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1170484</subfield>
<subfield code="z">md5:8329592ee64206a53d0118c24a817c6a</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/CTCF_2_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1870710</subfield>
<subfield code="z">md5:084a06bbb2faf37f2ef4dba006d6b748</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/CTCF_2_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1426624</subfield>
<subfield code="z">md5:67d94bf75af47ee6c319e7789b771c4a</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/CTCF_4_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">2296260</subfield>
<subfield code="z">md5:401f3bc4d14c2401942ee794caacdfdf</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/CTCF_4_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">2003600</subfield>
<subfield code="z">md5:fd306f4feb651b823ea41a328c331746</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/Rad21_0_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">3196623</subfield>
<subfield code="z">md5:7e9a1063b1035b5c380a0a45c067a311</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/Rad21_0_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">5230226</subfield>
<subfield code="z">md5:cf35d68fd1152a6f57d7e64a12dfda21</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/Rad21_2_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">8493481</subfield>
<subfield code="z">md5:06b0f603d7f805384b634185e5c066f3</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/Rad21_2_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">245357</subfield>
<subfield code="z">md5:19adbd5776b51f3e1e5fcac60259de75</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/Rad21_4_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">461970</subfield>
<subfield code="z">md5:37adc893b54466caa0cec2746a1fabf8</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/Rad21_4_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">2359669</subfield>
<subfield code="z">md5:da371dfbacac8e288052bb6b3d0777e8</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/WAPL_0_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">3716466</subfield>
<subfield code="z">md5:24bb4ec83206adb58bdc683f491addb1</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/WAPL_0_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">2037430</subfield>
<subfield code="z">md5:289d44dc3f417f8522c0588fbb989897</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/WAPL_4_hr.tagged_set.tsv</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">3043237</subfield>
<subfield code="z">md5:bb661e3b95d5691e7661551e4974e354</subfield>
<subfield code="u">https://zenodo.org/record/5770531/files/WAPL_4_hr.unfiltered.tagged_set.tsv</subfield>
</datafield>
<datafield tag="542" ind1=" " ind2=" ">
<subfield code="l">open</subfield>
</datafield>
<datafield tag="260" ind1=" " ind2=" ">
<subfield code="c">2021-12-09</subfield>
</datafield>
<datafield tag="909" ind1="C" ind2="O">
<subfield code="p">openaire_data</subfield>
<subfield code="o">oai:zenodo.org:5770531</subfield>
</datafield>
<datafield tag="100" ind1=" " ind2=" ">
<subfield code="u">Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139</subfield>
<subfield code="0">(orcid)0000-0002-5393-9084</subfield>
<subfield code="a">Gabriele, Michele</subfield>
</datafield>
<datafield tag="245" ind1=" " ind2=" ">
<subfield code="a">Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging</subfield>
</datafield>
<datafield tag="540" ind1=" " ind2=" ">
<subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield>
<subfield code="a">Creative Commons Attribution 4.0 International</subfield>
</datafield>
<datafield tag="650" ind1="1" ind2="7">
<subfield code="a">cc-by</subfield>
<subfield code="2">opendefinition.org</subfield>
</datafield>
<datafield tag="520" ind1=" " ind2=" ">
<subfield code="a"><p><strong>Overview</strong></p>
<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>
<ul>
<li>The cell lines and conditions used in this study</li>
<li>A summary of how the data was collected</li>
<li>The structure of the chromosome locus tracking data</li>
</ul>
<p><strong>Cell lines and conditions</strong></p>
<p>In total, the dataset covers 12 experimental conditions representing the following cell lines and treatment conditions:</p>
<ul>
<li>C36</li>
<li>C65</li>
<li>C27</li>
<li>CTCF-AID (untreated)</li>
<li>CTCF-AID (2 hours AID)</li>
<li>CTCF-AID (4 hours AID)</li>
<li>RAD21-AID (untreated)</li>
<li>RAD21-AID (2 hours AID)</li>
<li>RAD21-AID (4 hours AID)</li>
<li>WAPL-AID (untreated)</li>
<li>WAPL-AID (4 hours AID)</li>
<li>WAPL-AID (6 hours AID)</li>
</ul>
<p>&nbsp;</p>
<p><strong>Data and data processing</strong></p>
<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>
<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>
<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>
<p>File names are formatted follows.</p>
<ul>
<li>Quality controlled data have the structure: {Clone_and_condition_name}.tagged_set.tsv</li>
<li>Unfiltered data have the structure: {Clone_and_condition_name}.unfiltered.tagged_set.tsv</li>
</ul>
<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>
<p>&nbsp;</p>
<p><strong>Structure of Data</strong></p>
<p>The trajectory data are provided as tab-separated text files consisting of 10 columns. The column headers are:</p>
<ul>
<li>id: a unique dot pair index</li>
<li>t: the frame in which the dots were localized</li>
<li>x: x-coordinate of the dot in the EGFP channel (units in &micro;m)</li>
<li>y: y-coordinate of the dot in the EGFP channel (units in &micro;m)</li>
<li>z: z-coordinate of the dot in the EGFP channel (units in &micro;m)</li>
<li>x2: x-coordinate of the dot in the mScarlet channel (units in &micro;m)</li>
<li>y2: y-coordinate of the dot in the mScarlet channel (units in &micro;m)</li>
<li>z2: z-coordinate of the dot in the mScarlet channel (units in &micro;m)</li>
<li>dist: 3D distance between the dots across channels (units in &micro;m)</li>
<li>movie_index: an identifier used to link the dot pair back to the raw image timeseries.</li>
</ul></subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">isVersionOf</subfield>
<subfield code="a">10.5281/zenodo.5770530</subfield>
</datafield>
<datafield tag="024" ind1=" " ind2=" ">
<subfield code="a">10.5281/zenodo.5770531</subfield>
<subfield code="2">doi</subfield>
</datafield>
<datafield tag="980" ind1=" " ind2=" ">
<subfield code="a">dataset</subfield>
</datafield>
</record>
139
83
views
downloads
| All versions | This version | |
|---|---|---|
| Views | 139 | 139 |
| Downloads | 83 | 83 |
| Data volume | 273.1 MB | 273.1 MB |
| Unique views | 122 | 122 |
| Unique downloads | 16 | 16 |
Indexed in
- Publication date:
- December 9, 2021
- DOI:
-
- Keyword(s):
- Chromosome locus pair tracking CTCF depletion RAD21 depletion WAPL depletion Super-resolution live cell imaging Mouse embryonic stem cells
- License (for files):
- Creative Commons Attribution 4.0 International