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86 results for “Loop extrusion”
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 2/3
<p>Videos of cohesin translocation and collisions between translocating cohesin and MCMs under physiological salt conditions collected with MicroManager 1.4 as tif image sequences. Vidoes of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 1/3
<p>Videos of collisions between translocating cohesin and MCMs under high salt conditions collected with MicroManager 1.4 as tif image sequences. Vidoes of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 3/3
<p>Videos of collisions between translocating cohesin and MCM containing the YDF motif under physiological salt conditions collected with MicroManager 1.4 as tif image sequences. Videos of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging
<p><strong>Dataset description</strong></p> <p>This dataset contains coordinates of the two anchors of a 150 kb simulated loop (static imaging) and anchor-anchor distances of a 150 kb loop in simulations where the extruder was allowed to unbind from the polymer (dynamic imaging).</p> <p><strong>Dataset description - Static imaging</strong></p> <p>This dataset contains coordinates of the two anchors of a 150 kb simulated loop.</p> <p>The subfolder 'Free' contains coordinates from a polymer not submitted to loop extrusion (1,000 independent simulations). The subfolder 'Loop' contains loop anchor coordinates in a polymer submitted to loop extrusion (4,000 independent simulations). In simulations with extrusion, the polymer chain was simulated such as it went through 3 different states : i) Open state (absence of loops) ii) Extruding state where the loop size increases with time (anchor-anchor distance decreases) and iii) Closed state corresponding to a stable loop with the two anchors in contact.</p> <p> </p> <p><strong>Structure of data - Static imaging</strong></p> <p>In each .txt file, the first three columns correspond to the XYZ coordinates of the anchor (in µm), the fourth column indicates the state label (0=Open, 1=Extruding, 2=Closed). Each row corresponds to a simulation timepoint (2991 timepoints in polymers submitted to loop extrusion).</p> <p>The simulation ID is indicated at the end of each .txt file.</p> <p>The two anchors of the loop are bead #275 and bead #324.</p> <p> </p> <p><strong>Structure of data - Dynamic imaging</strong></p> <p>Each .txt file contains the anchor-anchor distance (in µm) as function of time for approximately 10,000 independent simulations. Each column is an independent simulation. Each row is a simulation timepoint (0.3 s / simulation unit). The different .txt files correspond to different localization errors, indicated in µm in XY and Z.</p> <p>'list_deb_closed_10000.p' is a dictionary whose keys are the simulation ID (corresponding to the columns of the .txt files), and the values are the frame at which extrusion begins.</p> <p>'list_end_closed_10000.p' is a dictionary whose keys are the simulation ID (corresponding to the columns of the .txt files), and the values are the frame at which extrusion ends.</p>
Dataset for 'A deep learning-based quality control loop of the extrusion-based bioprinting process'
<p>Zip file containing the dataset for the paper 'A deep learning-based quality control loop of the extrusion-based bioprinting process' (available at <a href="https://ijb.whioce.com/index.php/int-j-bioprinting/article/view/620">https://ijb.whioce.com/index.php/int-j-bioprinting/article/view/620</a>). The dataset is composed of:</p> <ul> <li>A series of video folders, each having a unique ID, and containing the processed video frames.</li> <li>A master.csv file containing all the metadata for each video.</li> </ul> <p>The authors acknowledge the supported by the European Union’s Horizon 2020 research and innovation program under the project GIOTTO: “Giotto: Active ageing and osteoporosis: The next challenge for smart nanobiomaterials and 3D technologies,” grant agreement no. 814410.</p>
Data analysis results for: "MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions"
<p>Due to technical issues we are unable to upload the updated version of this dataset on Zenodo.<br> <br> The latest version of this dataset can be found on the NRID research data archive at DOI <a href="https://doi.org/10.11582/2022.00056">10.11582/2022.00056</a>.</p>
CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire
Open the record for dataset details and reuse information.
Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [CSR-HTGTS-Seq]
GEO Series GSE130265. Mus musculus. 21 samples. Type: Genome variation profiling by high throughput sequencing.
RNA polymerases as moving barriers to condensin loop extrusion
GEO Series GSE117854. Bacillus subtilis PY79. 10 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [RNA-seq]
GEO Series GSE246367. Dictyostelium discoideum. 8 samples. Type: Expression profiling by high throughput sequencing.
Regulation of cohesin loop extrusion underlies changes in enhancer-promoter interactions during pancreatic cell differentiation
GEO Series GSE211101. Homo sapiens. 148 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching
GEO Series GSE130270. Mus musculus. 149 samples. Type: Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions
GEO Series GSE133228. Homo sapiens. 336 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by array.
Nuclear Morphology is Instructed by the Loop Extrusion Program [scRNA-seq]
GEO Series GSE211819. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [ChIP-Seq]
GEO Series GSE130213. Mus musculus. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Characterization of induced cohesin loop extrusion trajectories in living cells [BrU-seq]
GEO Series GSE278397. Homo sapiens. 9 samples. Type: Other.
Wapl repression by Pax5 promotes loop extrusion and V gene recombination at the Igh locus
GEO Series GSE140975. Mus musculus. 170 samples. Type: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers [HiC]
GEO Series GSE182105. Homo sapiens. 9 samples. Type: Other.
Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers [Repli-seq]
GEO Series GSE182107. Homo sapiens. 8 samples. Type: Other.
Genome-wide in vivo dynamics of cohesin-mediated loop extrusion and its role in transcription activation
GEO Series GSE277721. Homo sapiens. 168 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
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International Brain Laboratory public data
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OpenNeuro
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