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Dataset results
13 results for “motile cilia”
Cilia density and flow velocity affect alignment of motile cilia from brain cells
<p>Here we store the supplementary Materials and Methods for the publication Cilia density and flow velocity affect alignment of motile cilia from brain cells.</p> <p>In the Supplementary methods we included additional information on the hydrodynamic simulations. </p> <p>Video1 and Video2 are videos referenced in the main text of the paper</p> <p>In the archive 'raw data and code.tar' , we provide raw images and codes to support the article.The complete dataset of raw images is more than 1 Tb. Here we are limited to 50Gb. The full dataset is available upon request.<br> <br> We choose to provide a full dataset of two culture at DIV 16, one treated with shear flow and a control without flow.</p> <p>For each of the two cultures, the videos with propelled particles are in the directory FL,<br> The bright field images without particles are stored in BF. Unfortunately we uploaded only few videos because of their large size. The results of the analysis of this dataset is reported in the directory analysis (available for each culture).</p> <p>Moreover we provide the code to analyse these data.<br> The analysis routine:</p> <p>Step 1: for each field of view (fov) getting the cilia beating direction from the FL images. This is done with PIV. The code is Step1_PIVanalysis.mat</p> <p>Step 2: for each fov getting ciliated cell position and CBF from the BF movies. Gather the cilia beating direction and cilia posion and frequency in a unique figure and matlab class (Res.mat). This is done in Step2_gatherResults.mat</p> <p>The results of these analysis are stored in the analysis folder for each culture.</p> <p>These routines are repeated for each experiment and results are then plotted to get trends. In the folder code4figures we report the code that we used to make the figures in the papers starting from a matlab file "all_results*.mat", where are gathered all the analysis.</p> <p>The code may improve in the future with more comments. please check Nicola's github page for the latest update. Please contact us for any problem. https://github.com/NicolaPellicciotta/Code4-Cilia-density-and-flow-velocity-affect-alignment-of-motile-cilia-from-brain-cells</p> <p>All the raw videos and code are in the archive.</p> <p> </p>
Dataset for: Entrainment of mammalian motile cilia in the brain with hydrodynamic forces
<p>Please read the README.md for information on how to handle the dataset.</p>
Video for: The role of hydrodynamic forces in synchronisation and alignment of mammalian motile cilia
<p>Here you can find all the videos of the PhD thesis: </p> <p>The role of hydrodynamic forces in synchronisation and alignment of mammalian motile cilia.</p> <p>by Nicola Pellicciotta</p> <p>Video1: This example shows a movie of a single cell, being subjected to an external oscillatory flow. Images were acquired at 500\,fps using a 60X objective, then analysed using background subtraction and spatial median filter of 3x3 pixels. Chapter 3</p> <p>Video 2: we show the entrainment of a group of cells with very strong oscillatory external flow $v_\mathrm{EX}= 2$\,mm/s at $f_\mathrm{EX}=12$\,Hz. This s flow induced entrainment and also alignment of beating direction of some cells that were beating misaligned to the external flow. The original direction of beating was recovered after the flow stopped. Chapter 3</p> <p>Video3 and Video4: we depolymerised cell actin by adding 2uM Cytochalasin-D in the cell culture medium for 48hr. After imaging, cells (control and dug treated) were stained in 4\% PFA for 10 minutes, permeabilised with Triton x-100 0.1\% in PBS, and incubated for 1 hour with Nucblue R37605 (1 drop for mL of PBS) and with phalloidin for actin (Sir-Actin, 0.2 uM) following proprietary protocols. Z-stack were taken with confocal microscope (slices of distance of 0.15um each) and can be found at the following links: DMSO treated cells (control) Video 3, and Cytochalasin-D treated, Video 4. Chapter 3</p> <p>Video5: The maximal beating amplitude for a cilium within each cell was measured by inspecting the recordings from top view and marking two extreme points at the power and recovery stroke. Chapter 3</p> <p>Video6: Experimental procedure and the image analysis methods for Chapter 4. Continuous fluid flow is applied for three days on cells cultured in Transwell-chips. The chips are then removed from the flow and cilia motility is imaged with the microscope. From high speed Bright Field movies we identify ciliary beating frequency and cell position, while from tracer particles we measure ciliary beating direction. </p> <p>Video7: Video of Propelled particles in a culture at 29 DIV and treated with shear stress τ ≈0.8 dyne/cm2. Chapter 4</p> <p> </p>
Dataset for: Motile cilia hydrodynamics: Entrainment versus synchronisation when coupling through flow
<p>This archive contains the dataset for the article "Motile cilia hydrodynamics: Entrainment versus synchronisation when coupling through flow".</p> <p>We gathered videos of cilia dynamics from different sources. For each animal/microorganism we upload the videos in different formats depending on the source:</p> <p>- .tiffs usually in a directory, it is composed by a series of images</p> <p>- .movie a format that we use in our lab and that it is combatible with our software in Matlab to tack cilium waveform</p> <p>- .avi </p> <p>For each video we also have the results from the tracking with our software. The resuts from a single video are all in a Matlab variable that has the same name but with the extension .clclk_force</p> <p>for example for the video "filename", the results are in "filename.clclk_force".<br> In Matlab these can be loaded as force = load('filename.clclk_force','-mat');<br> For all the videos these can be directly be found in the directory cilium waveforms force files.</p>
Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [RNA-Seq]
GEO Series GSE132116. Xenopus laevis. 25 samples. Type: Expression profiling by high throughput sequencing.
Cerebrospinal fluid-driven ependymal motile cilia defects are implicated in multiple sclerosis pathophysiology
GEO Series GSE301791. Rattus norvegicus. 7 samples. Type: Expression profiling by high throughput sequencing.
Schizophrenia-related microdeletion causes progressive brain ventricle enlargement through microRNA-dependent deceleration of motile cilia beating
GEO Series GSE123560. Mus musculus. 16 samples. Type: Non-coding RNA profiling by array.
Cerebrospinal fluid-driven ependymal motile cilia defects are implicated in multiple sclerosis pathophysiology
GEO Series GSE301585. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility
GEO Series GSE132117. Mus musculus; Xenopus laevis. 33 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain
GEO Series GSE254006. Danio rerio. 8 samples. Type: Expression profiling by high throughput sequencing.
Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [ChIP-Seq]
GEO Series GSE132115. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Strain-specific differences in brain gene expression in a hydrocephalic mouse model with motile cilia dysfunction
GEO Series GSE113233. Mus musculus. 12 samples. Type: Expression profiling by array.
The Ciliary GTPase ARL13B maintains Ductule Physiology through the Primary and Motile Cilia in Male Reproduction
GEO Series GSE256400. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.