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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    <subfield code="a">&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;
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