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Dataset results
51 results for “cell monolayer”
NEUBIAS TS7 - data used in the workflow deconstruction session on quantifying monolayer cell migration
<p>Training session details (including slides): https://github.com/miura/NEUBIAS_AnalystSchool2018/tree/master/Assaf</p> <p>Matlab source code: https://github.com/assafzar/MonolayerKymographs</p>
Cell Monolayer Friction Data 1
<p>In this work an improved test bed to simulate tissue including an endothelial cell (HUVEC) monolayer was developed and tested in a sliding friction test using different probe materials.</p>
Cell Monolayer Friction Data 2
<p>In this work an improved test bed to simulate tissue including an endothelial cell (HUVEC) monolayer was developed and tested in a sliding friction test using different probe materials.</p>
Molecular-scale substrate anisotropy, crowding, and division drive collective behaviors in cell monolayers
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Data and code for "Migration and division in cell monolayers on substrates with topological defects"
<p>Raw data for experiment (experiment.zip) and basic simulation code (simulation.zip) for the paper "Migration and division in cell monolayers on substrates with topological defects"</p>
Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density.
<p>Raw data files concerning the publication,</p> <p><strong>Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density</strong><br>Julia Eckert, Benoit Ladoux, Rene-Marc Mege, Luca Giomi and Thomas Schmidt<br>Nature Communications (2023) <strong>14</strong>:5762.<br>doi: <span>https://doi.org/10.1038/s41467-023-41449-6</span><br><br><strong>Abstract:</strong></p> <p>Changes in tissue geometry during developmental processes are associated with collective migration of cells. Recent experimental and numerical results suggest that these changes could leverage on the coexistence of nematic and hexatic orientational order at different length scales. How this multiscale organization is affected by the material properties of the cells and their substrate is presently unknown. In this study, we address these questions in monolayers of Madin-Darby canine kidney cells having various cell densities and molecular repertoires. At small length scales, confluent monolayers are characterized by a prominent hexatic order, independent of the presence of E-cadherin, monolayer density, and underlying substrate stiffness. However, all three properties affect the meso-scale tissue organization. The length scale at which hexatic order transits to nematic order, the ”hexanematic” crossover scale, strongly depends on cell-cell adhesions and correlates with monolayer density. Our study demonstrates how epithelial organization is affected by mechanical properties, and provides a robust description of tissue organization during developmental processes.</p> <p> </p> <p><strong>Data description:</strong></p> <p>WT.zip - zipped raw image data and extracted vertices of experiments on wild-type cells<br>KO.zip - zipped raw image data and extracted vertices of experiments on eCad KO-cells<br>FigureData.zip - zipped data referring to each of the figures in the paper</p> <p> </p> <p><strong>Software:</strong></p> <p>The software to analyze the data presented here is found on GitHub, [https://github.com/hexanematic/orientation tracker]</p>
Quantifying monolayer cell migration sample dataset
<p>The sample data to use with the Quantifying monolayer cell migration chapter of the 'Bioimage Data Analysis Workflows - Advanced Components and Methods' Neubias textbook.</p>
Data from: Sources of variability in cytosolic calcium transients triggered by stimulation of homogeneous uro-epithelial cell monolayers
Epithelial tissue structure is the emergent outcome of the interactions between large numbers of individual cells. Experimental cell biology offers an important tool to unravel these complex interactions, but current methods of analysis tend to be limited to mean field approaches or representation by selected subsets of cells. This may result in bias towards cells that respond in a particular way and/or neglect local, context-specific cell responses. Here, an automated algorithm was applied to examine in detail the individual calcium transients evoked in genetically homogeneous, but asynchronous populations of cultured non-immortalized normal human urothelial cells when subjected to either the global application of an external agonist or a localized scratch wound. The recorded calcium transients were classified automatically according to a set of defined metrics and distinct sub-populations of cells that responded in qualitatively different ways were observed. The nature of this variability in the homogeneous cell population was apportioned to two sources: intrinsic variation in individual cell responses and extrinsic variability due to context-specific factors of the environment, such as spatial heterogeneity. Statistically significant variation in the features of the calcium transients evoked by scratch wounding according to proximity to the wound edge was identified. The manifestation of distinct sub-populations of cells is considered central to the coordination of population-level response resulting in wound closure.
Data from: Sources of variability in cytosolic calcium transients triggered by stimulation of homogeneous uro-epithelial cell monolayers
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Multiplexed single cell mRNA sequencing of monolayer- and organoid-system differentiated cells derived from human iPSC with and without NKX2-5 genetic manipulations
GEO Series GSE163619. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Highly functional intestinal monolayer through organoids derived from human iPS cells for drug discovery research
GEO Series GSE240322. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Comparative analysis of gene expression of cell line DU145 grown under sphere forming condition and as monolayer
GEO Series GSE148013. Homo sapiens. 12 samples. Type: Expression profiling by array.
Single cell analysis of Monolayer and Organoid Primary Prostate Human Epithelial Cells Derived from the same patient
GEO Series GSE130318. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome Analysis of Non-Human Primate Induced Pluripotent Stem Cell-Derived Cardiomyocytes in 2D Monolayer Culture versus 3D Engineered Heart Tissue
GEO Series GSE156237. Macaca mulatta. 12 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profiling of 1205Lu human melanoma cells after reversible shifting between monolayer and stem cell-like growth
GEO Series GSE62849. Homo sapiens. 3 samples. Type: Expression profiling by array.
Canine hemangiosarcoma tissues, monolayer- and sphere-cultured cells
GEO Series GSE53219. Canis lupus familiaris. 42 samples. Type: Expression profiling by array.
Single -cell transcriptomic profiling of stem cell derived retinal pigment epithelial cell monolayers after subretinal transplantation
GEO Series GSE212896. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
FRT thyroid cells: 2D monolayers vs. 3D follicles
GEO Series GSE71259. Rattus norvegicus. 5 samples. Type: Expression profiling by array.
Epigenetic remodeling during monolayer cell expansion reduces regeneration potential
GEO Series GSE190339. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA sequencing analysis of HUVEC in monolayer alone or exposed to (bacterially-infected) macrophage-like U937 cells for 8 h.
GEO Series GSE312719. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.