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.
JSON Export
{
"files": [
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/C27.tagged_set.tsv"
},
"checksum": "md5:69339440363357be7beda98611cf4ac4",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "C27.tagged_set.tsv",
"type": "tsv",
"size": 3615980
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/C27.unfiltered.tagged_set.tsv"
},
"checksum": "md5:6fd8c436d0b6411d406520738a981027",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "C27.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 5358430
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/C36.tagged_set.tsv"
},
"checksum": "md5:5b45eee20c1a4c6c3c7a07caa4bd13f6",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "C36.tagged_set.tsv",
"type": "tsv",
"size": 5192863
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/C36.unfiltered.tagged_set.tsv"
},
"checksum": "md5:834d0b996a5ea633e586c6bb4f538f1d",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "C36.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 7906793
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/C65.tagged_set.tsv"
},
"checksum": "md5:f2fc3e9ffbdf8e82639f58b65eb6a615",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "C65.tagged_set.tsv",
"type": "tsv",
"size": 1519038
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/C65.unfiltered.tagged_set.tsv"
},
"checksum": "md5:7d8597533cd513bae8db2618214b0950",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "C65.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 2129493
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/CTCF_0_hr.tagged_set.tsv"
},
"checksum": "md5:0b5baa2fbb5c4753ea7bafdf02c6e773",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "CTCF_0_hr.tagged_set.tsv",
"type": "tsv",
"size": 1301164
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/CTCF_0_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:e334a17ec1c17393fd7d98e4e0df23a2",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "CTCF_0_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 1970691
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/CTCF_2_hr.tagged_set.tsv"
},
"checksum": "md5:8329592ee64206a53d0118c24a817c6a",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "CTCF_2_hr.tagged_set.tsv",
"type": "tsv",
"size": 1170484
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/CTCF_2_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:084a06bbb2faf37f2ef4dba006d6b748",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "CTCF_2_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 1870710
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/CTCF_4_hr.tagged_set.tsv"
},
"checksum": "md5:67d94bf75af47ee6c319e7789b771c4a",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "CTCF_4_hr.tagged_set.tsv",
"type": "tsv",
"size": 1426624
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/CTCF_4_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:401f3bc4d14c2401942ee794caacdfdf",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "CTCF_4_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 2296260
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/Rad21_0_hr.tagged_set.tsv"
},
"checksum": "md5:fd306f4feb651b823ea41a328c331746",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "Rad21_0_hr.tagged_set.tsv",
"type": "tsv",
"size": 2003600
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/Rad21_0_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:7e9a1063b1035b5c380a0a45c067a311",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "Rad21_0_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 3196623
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/Rad21_2_hr.tagged_set.tsv"
},
"checksum": "md5:cf35d68fd1152a6f57d7e64a12dfda21",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "Rad21_2_hr.tagged_set.tsv",
"type": "tsv",
"size": 5230226
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/Rad21_2_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:06b0f603d7f805384b634185e5c066f3",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "Rad21_2_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 8493481
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/Rad21_4_hr.tagged_set.tsv"
},
"checksum": "md5:19adbd5776b51f3e1e5fcac60259de75",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "Rad21_4_hr.tagged_set.tsv",
"type": "tsv",
"size": 245357
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/Rad21_4_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:37adc893b54466caa0cec2746a1fabf8",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "Rad21_4_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 461970
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/WAPL_0_hr.tagged_set.tsv"
},
"checksum": "md5:da371dfbacac8e288052bb6b3d0777e8",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "WAPL_0_hr.tagged_set.tsv",
"type": "tsv",
"size": 2359669
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/WAPL_0_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:24bb4ec83206adb58bdc683f491addb1",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "WAPL_0_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 3716466
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/WAPL_4_hr.tagged_set.tsv"
},
"checksum": "md5:289d44dc3f417f8522c0588fbb989897",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "WAPL_4_hr.tagged_set.tsv",
"type": "tsv",
"size": 2037430
},
{
"links": {
"self": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b/WAPL_4_hr.unfiltered.tagged_set.tsv"
},
"checksum": "md5:bb661e3b95d5691e7661551e4974e354",
"bucket": "fab90d03-5259-480e-9a83-3e9a5f003e1b",
"key": "WAPL_4_hr.unfiltered.tagged_set.tsv",
"type": "tsv",
"size": 3043237
}
],
"owners": [
234132
],
"doi": "10.5281/zenodo.5770531",
"stats": {
"version_unique_downloads": 16.0,
"unique_views": 122.0,
"views": 139.0,
"version_views": 139.0,
"unique_downloads": 16.0,
"version_unique_views": 122.0,
"volume": 273056209.0,
"version_downloads": 83.0,
"downloads": 83.0,
"version_volume": 273056209.0
},
"links": {
"doi": "https://doi.org/10.5281/zenodo.5770531",
"conceptdoi": "https://doi.org/10.5281/zenodo.5770530",
"bucket": "https://zenodo.org/api/files/fab90d03-5259-480e-9a83-3e9a5f003e1b",
"conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.5770530.svg",
"html": "https://zenodo.org/record/5770531",
"latest_html": "https://zenodo.org/record/5770531",
"badge": "https://zenodo.org/badge/doi/10.5281/zenodo.5770531.svg",
"latest": "https://zenodo.org/api/records/5770531"
},
"conceptdoi": "10.5281/zenodo.5770530",
"created": "2021-12-09T16:54:02.458188+00:00",
"updated": "2021-12-10T01:48:45.555093+00:00",
"conceptrecid": "5770530",
"revision": 2,
"id": 5770531,
"metadata": {
"access_right_category": "success",
"doi": "10.5281/zenodo.5770531",
"description": "<p><strong>Overview</strong></p>\n\n<p>This repository contains all the raw and processed trajectory data associated with “paper title”. 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> </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 µm x 49.69 µm (584 x 584 pixels, pixel size: 0.085 µm by 0.085 µm), 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 µm, for a total height of 7.25 µm. 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 “unfiltered” 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 “”.</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 “0 hours” as the tag. Thus, the RAD21 (untreated) becomes RAD21_0_hr.tagged_set.tsv.</p>\n\n<p> </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 µm)</li>\n\t<li>y: y-coordinate of the dot in the EGFP channel (units in µm)</li>\n\t<li>z: z-coordinate of the dot in the EGFP channel (units in µm)</li>\n\t<li>x2: x-coordinate of the dot in the mScarlet channel (units in µm)</li>\n\t<li>y2: y-coordinate of the dot in the mScarlet channel (units in µm)</li>\n\t<li>z2: z-coordinate of the dot in the mScarlet channel (units in µm)</li>\n\t<li>dist: 3D distance between the dots across channels (units in µm)</li>\n\t<li>movie_index: an identifier used to link the dot pair back to the raw image timeseries.</li>\n</ul>",
"license": {
"id": "CC-BY-4.0"
},
"title": "Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging",
"notes": "MG, HBB, SGH contributed equally to this study.",
"relations": {
"version": [
{
"count": 1,
"index": 0,
"parent": {
"pid_type": "recid",
"pid_value": "5770530"
},
"is_last": true,
"last_child": {
"pid_type": "recid",
"pid_value": "5770531"
}
}
]
},
"version": "1.0",
"keywords": [
"Chromosome locus pair tracking",
"CTCF depletion",
"RAD21 depletion",
"WAPL depletion",
"Super-resolution live cell imaging",
"Mouse embryonic stem cells"
],
"publication_date": "2021-12-09",
"creators": [
{
"orcid": "0000-0002-5393-9084",
"affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139",
"name": "Gabriele, Michele"
},
{
"orcid": "0000-0001-5496-0638",
"affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139",
"name": "Brand\u00e3o, Hugo B."
},
{
"orcid": "0000-0002-0717-5757",
"affiliation": "Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA",
"name": "Grosse-Holz, Simon"
},
{
"orcid": "0000-0002-2612-551X",
"affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139",
"name": "Jha, Asmita"
},
{
"orcid": "0000-0002-8988-963X",
"affiliation": "Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA",
"name": "Dailey, Gina M."
},
{
"orcid": "0000-0001-6100-0491",
"affiliation": "Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA",
"name": "Cattoglio, Claudia"
},
{
"orcid": "0000-0003-2094-0772",
"affiliation": "Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA",
"name": "Hsieh, Tsung-Han S."
},
{
"orcid": "0000-0002-0785-5410",
"affiliation": "Department of Physics and Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA",
"name": "Mirny, Leonid"
},
{
"orcid": "0000-0003-1300-6076",
"affiliation": "Max Planck Institute of Molecular Cell Biology & Genetics; Dresden, Germany",
"name": "Zechner, Christoph"
},
{
"orcid": "0000-0001-7540-7858",
"affiliation": "Department of Biological Engineering, Massachusetts Institute of Technology;, Cambridge, 02139",
"name": "Hansen, Anders S."
}
],
"access_right": "open",
"resource_type": {
"type": "dataset",
"title": "Dataset"
},
"related_identifiers": [
{
"scheme": "doi",
"identifier": "10.5281/zenodo.5770530",
"relation": "isVersionOf"
}
]
}
}
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