Dataset
Uniform dynamics of cohesin-mediated loop extrusion
| Τίτλος: | Uniform dynamics of cohesin-mediated loop extrusion |
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| Συγγραφείς: | Sabaté, Thomas, Lelandais, Benoît, Robert, Marie-Cécile, Szalay, Michael, Tinevez, Jean-Yves, Bertrand, Edouard, Zimmer, Christophe |
| Στοιχεία εκδότη: | Zenodo |
| Έτος έκδοσης: | 2025 |
| Συλλογή: | Zenodo |
| Περιγραφή: | Overview This repository contains all the raw and quality-controlled distance times series associated with the study "Universal dynamics of cohesin-mediated loop extrusion", as well as the code to analyze them. Here, we provide the following information: The cell lines and conditions used in this study A summary of how the data was collected and processed The structure of the distance time series Cell lines and conditions In total, the dataset covers 14 experimental conditions with 5 different cell lines, 2 different treatments, and 2 different imaging acquisition frequencies, listed hereafter as (Cell line; Treatment; Frequency): L1; - Auxin L1; + Auxin 2h L2; - Auxin L2; + Auxin 2h T1; - Auxin T1; + Auxin 2h Half TAD; - Auxin Half TAD; + Auxin 2h Adjacent; - Auxin L2; - Auxin; High frequency L2; + Auxin 2h; High frequency Half TAD; - Auxin; High frequency Half TAD; + Auxin 2h; High frequency Adjacent; - Auxin; High frequency Data and data processing Time lapse image acquisition was performed with an inverted microscope (Nikon) coupled to the Dragonfly spinning disk (Andor) using a 100X Plan Apo 1.45 NA oil immersion objective. Excitation sources were 488 nm (150 mW) and 637 nm (140 mW) lasers. Exposure time was set to 85 ms for both channels with 1% laser power in far-red and 5-8% laser power in the GFP channel depending on the imaged cell line. Z-stacks of 29 optical slices separated by 0.29 µm each were acquired every 30 s (or every 9 s for 'HighFreq' datasets) using the perfect focus system and five different stage positions were imaged for each 2-hour (or 36 min for 'HighFreq' datasets) acquisition. The two channels were acquired simultaneously on two distinct EMCCD iXon888 cameras (1024 x 1024 pixels, effective pixel size: 0.121 µm). The 3D image time series were processed as described at https://github.com/imodpasteur/Sabate_et_al_TAD_Anchors/tree/main/Live-cell_analysis/Image_processing to obtain time series of 3D distances from live-cell microscopy images of TAD anchors. Time series have been corrected ... |
| Τύπος εγγράφου: | dataset |
| Γλώσσα: | unknown |
| Relation: | https://zenodo.org/records/16949930; oai:zenodo.org:16949930; https://doi.org/10.5281/zenodo.16949930 |
| DOI: | 10.5281/zenodo.16949930 |
| Διαθεσιμότητα: | https://doi.org/10.5281/zenodo.16949930 https://zenodo.org/records/16949930 |
| Rights: | Creative Commons Attribution 4.0 International ; cc-by-4.0 ; https://creativecommons.org/licenses/by/4.0/legalcode |
| Αριθμός Καταχώρησης: | edsbas.BD776AA0 |
| Βάση Δεδομένων: | BASE |
| DOI: | 10.5281/zenodo.16949930 |
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