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1,248 results for “epithelium”
Underlying data for: "Capturing the mechanosensitivity of cell proliferation in models of epithelium"
<p>For our publication "Capturing the mechanosensitivity of cell proliferation in models of epithelium" (available as a preprint at <a title="BioRXiv Link" href="https://doi.org/10.1101/2023.01.31.526438" target="_blank" rel="noopener">DOI: 10.1101/2023.01.31.526438 )</a> we here provide the raw data for the included plots and the code used to generate the Delayed Fisher Kolmogorov (DFK) data referenced in the main publication</p> <p>The archive '<em>underlying_data.zip</em>' contains raw data underlying the plots in the publication. <br>The archive '<em>puls_proliferation_rate-1.0.zip</em>' contains the code for generating DFK trajectories referenced in the publication and its SI. <br>The archive '<em>ddesolver-1.0.zip</em>' contains the python code for solving delayed differential equations used by the puls_proliferation_rate project. It is included to ensure completeness and reproducibility of the simulations. </p>
Zellige example dataset: inner ear organoid epithelium
<p><strong>Inner ear organoid at day 14 of culture. </strong></p> <p>The z-stack image encompasses half of the spherical organoid including two distinct and superimposed surfaces that correspond to the basal side of the epithelium and the apical junctional network. It was acquired with a confocal microscope (Nikon A1HD25) equipped with a Nikon Plan-Apochromat 25x lens (NA=1.05). Pixel size 0.690 µm, z step >1 µm. This dataset contains both the ground-truth height maps and the height maps generated with Zellige. The Zellige parameters used are:</p> <p><span class="math-tex">\(T_{A}=5, T_{otsu}=12, S_{min}=5, \sigma_{xy}=2, \sigma_{z}=1, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.8, T_{OSE2}=0.1, R_{2}=10, C_{2}=0.8.\)</span></p> <p>Nota: to compare the ground truth height map with the Zellige height map, one first needs to substrat 1 to all values of the Zellige height map.</p> <p>See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau <em>et al.</em> 2022: <a href="https://doi.org/10.1101/2022.04.05.485876">https://doi.org/10.1101/2022.04.05.485876</a></p>
PESO: Prostate Epithelium Segmentation on H&E-stained prostatectomy whole slide images
<p>Large set of whole-slide-images (WSI) of prostatectomy specimens with various grades of prostate cancer (PCa). More information can be found in the corresponding paper: <a href="https://doi.org/10.1038/s41598-018-37257-4">https://doi.org/10.1038/s41598-018-37257-4</a></p> <p>The WSIs in this dataset can be viewed using the open-source software <a href="https://github.com/computationalpathologygroup/ASAP">ASAP</a> or <a href="https://openslide.org/">Open Slide</a>.</p> <p>Due to the large size of the complete dataset, the data has been split up in to multiple archives.</p> <p>The data from the training set:</p> <ul> <li><strong>peso_training_masks.zip: </strong>Training masks (N=62) that have been used to train the main network of our paper. These masks are generated by a trained U-Net on the corresponding IHC slides.</li> <li><strong>peso_training_masks_corrected.zip: </strong>A subset of the color deconvolution masks (N=25) on which manual annotations have been made. Within these regions, stain and other artifacts have been removed.</li> <li><strong>peso_training_colordeconvolution.zip: </strong>Mask files (N=62) containing the P63&CK8/18 channel of the color deconvolution operation. These masks mark all regions that are stained by either P63 or CK8/18 in the IHC version of the slides.</li> <li><strong>peso_training_wsi_{1-6}.zip: </strong>Zip files containing the whole slide images of the training set (N=62). Each archive contains 10 slides, excluding the last which contains 12. These images are exported at a pixel resolution of 0.48mu/pixels. </li> </ul> <p>The data from the test set:</p> <ul> <li><strong>peso_testset_regions.zip: </strong>Collection of annotation XML files with outlines of the test regions. These can be used to view the test regions in more detail using ASAP.</li> <li><strong>peso_testset_png.zip: </strong>Export of the test set regions in PNG format (2500x2500 pixels per region).</li> <li><strong>peso_testset_png_padded.zip: </strong>Export of the test regions in PNG format padded with a 500 pixel wide border (3500x3500 pixels per region). Useful for segmenting pixels at the border of the regions.</li> <li><strong>peso_testset_mapping.csv: </strong>A csv file mapping files from the test set (numbered 1-160) to regions in the xml files. The csv file also contains the label (benign or cancer) for each region.</li> <li><strong>peso_testset_groundtruth_masks.zip: </strong>The ground truth (pixel) masks (N=40) of all regions in the test set. For each pixel in the test set regions, these masks contain the ground truth: 0 for unlabelled, 1 for background and 2 for epithelial tissue.</li> <li><strong>peso_testset_wsi_{1-4}.zip: </strong>Zip files containing the whole slide images of the test set (N=40). Each archive contains 10 slides of the test set. These images are exported at a pixel resolution of 0.48mu/pixels. </li> </ul> <p>This study was financed by a grant from the Dutch Cancer Society (KWF), grant number KUN 2015-7970.</p> <p><strong>If you make use of this dataset please cite both the dataset itself and the corresponding paper: </strong><a href="https://doi.org/10.1038/s41598-018-37257-4">https://doi.org/10.1038/s41598-018-37257-4</a></p> <p><strong>Update July 2021: </strong>We have added the ground truth masks for the test set.</p>
Raw data: Patterned apoptosis has an instructive role for local growth and tissue shape regulation in a fast-growing epithelium
<p>What regulates organ size and shape remains one fundamental mystery of modern biology. Research in this area has primarily focused on deciphering the regulation in time and space of growth and cell division, while the contribution of cell death has been overall neglected. This includes studies of the <i>Drosophila</i> wing, one of the best characterised systems for the study of growth and patterning, undergoing massive growth during larval stage and important morphogenetic remodeling during pupal stage. So far, it has been assumed that cell death was relatively neglectable in this tissue both during larval and pupal stage and as a result the pattern of growth was usually attributed to the distribution of cell division. Here, using systematic mapping and registration combined with quantitative assessment of clone size and disappearance as well as live imaging, we outline a persistent pattern of cell death and clone elimination emerging in the larval wing disc and persisting during pupal wing morphogenesis. Local variation of cell death is associated with local variation of clone size, pointing to an impact of cell death on local growth which is not fully compensated by proliferation. Using morphometric analyses of adult wing shape and genetic perturbations, we provide evidence that patterned death affects locally and globally adult wing shape and size. This study describes a roadmap for precise assessment of the contribution of cell death to tissue shape, and outlines an important instructive role of cell death in modulating quantitatively local growth and morphogenesis of a fast-growing tissue.</p><p>This repository contains the raw data (local projection images, ROI and quantificatiosn) of the Current Biology article "<strong>Patterned apoptosis has an instructive role for local growth and tissue shape regulation in a fast-growing epithelium".</strong></p>
Fig. 1 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 1. Photomicrographs of the olfactory epithelium of Pygocentrus nattereri by scanning electron microscopy (SEM) and histological architecture stained with Delafield's Haematoxylin-Eosin (HE) and Mallory's triple (MT) stain. A — oval shaped olfactory rosette showing olfactory lamellae (OL) radiating from median raphe (R). Note tongue shaped structure (arrow heads) on the apical end of the lamellae (SEM) ×50. B — sensory olfactory epithelium (OEP) lined with receptor cells. Note the presence of blood vessels (BV) in the central core (CC) which is distinguished from OEP by basement membrane (BM). Arrow heads indicate basal cells above BM (MT) ×400. C — higher magnification of OEP showing a large number of primary receptor cells (RC) with conspicuous nuclei (N), secondary recptor cells (broken arrows), microvillous cells (MV) intermingled with supporting cells (SC). Note the presence of BV in CC and BC (arrow heads) near CC. Solid arrow indicates the axons of secondary RC communicate to CC (MT) ×1000. D — OEP exhibiting cylindrical RC with knob like vesicles (black arrow heads), ciliated supporting cells (solid arrows), non-ciliated supporting cells (white arrow heads) and BC above CC. Broken arrows mark the cilia of supporting cells on the epithelial surface (HE) ×400. E — tuft of receptor cells (RC) in between supporting cells (SC) (SEM) ×4000. F — dendrite patches of RC (broken arrows) and microvillous cells (solid arrows) in between stratified epithelial cells (SEC). Note the opening of mucous cells (arrow heads) in between SEC (SEM) ×2500.
Fig. 2 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 2. Photomicrographs of the olfactory epithelium of P. nattereri by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and histological features stained with Mallory's triple (MT) stain. A — transitional zone between sensory epithelium (SE) with receptor cells (solid arrows) and non-sensory epithelium (NSE) having a series of mucous cells (MC) (Broken arrows), labyrinth cells (LC) and stratified epithelial cells (arrow heads). Olfactory epithelium separated from central core (CC) by a basement membrane (BM) (MT) ×400. B — surface of non-sensory epithelium showing densely arranged ciliated supporting cells (solid arrows) encircled the non-ciliated supporting cells (SC) with adhering mucin mass (arrow heads). Note the opening of MC (broken arrows) in between SC (SEM) ×4500. C — dendrite of receptor cell (RC) emerging out from basal body (broken arrow). Note microtubules of rod (solid arrow) parallel arranged (TEM) ×5000. D —nuclei of receptor cells (N) showing dispersed heterochromatin (arrow heads). Note the presence of mitochondria (solid arrows) adjacent to nucleus (TEM) ×500. (E) Showing cisterns of rough endoplasmic reticulum (rER) (arrow heads) encircling nucleus (solid arrow). Note Golgi apparatus (broken arrow) adjacent to rER (TEM) ×4000. F — OEP lined with microvillous cells (MV), mucous cell (MC) and supporting cell (broken arrow) (TEM) ×2100. G — microvillous cells exhibiting abundant ribosomes (broken arrows) and extended mitochondria (arrow heads). Solid arrow indicates nucleus (TEM) ×5000. H — axons (broken arrows) of receptor cells run parallel on both sides of basal cells (solid arrow) (TEM) ×5000.
Fig. 3 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 3. Photomicrographs of the olfactory epithelium of P. nattereri by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). A — olfactory epithelium (OEP showing mucous cell (MC) having granules, microvillous cell (arrow head), labyrinth cell (broken arrow) and vesicular cytoplasm of supporting cell (solid arrow) (TEM) ×2100. B — flat surface ciliated supporting cell (solid arrow) provided with plenty of kinocilia (arrow heads) showing microtubular pattern (broken arrows). Note large number of mitochondria within the cytoplasm of supporting cells (TEM) ×5000. C — non-sensory olfactory epithelium (OEP) comprised of MC filled with large granules and supporting cells (solid arrows) (TEM) ×2100. D — basal cells provided with conspicuous lobular nuclei (N) having dense nucleolus (solid arrow). Note the presence of small vesicles (arrow head) adjacent the nucleus and rough endoplasmic reticulum (rER) (broken arrows) (TEM) ×2500. E — showing nuclear division of basal cells provided with dense nucleus (solid arrows). Broken arrows indicate mature nucleus of basal cells (TEM) ×2500. F — showing labyrinth cells (solid arrow) with conspicuous folding encircled by compactly arranged stratified epithelial cells (SEC). Note the presence of MC (broken arrows) in between SEC and mucin droplets (arrow heads) over SEC (SEM) ×4500. G — surface epithelium of raphe provided with packed SEC having labyrinth pattern microridges. Note the presence of opening of MC (solid arrows) and mucin droplets (arrow heads) over SEC (SEM) ×4500. H — raphe showing oval and elongated nuclei (N) of Stratified epithelial cells. Note the presence of rER (solid arrows) and vesicles (broken arrows) adjacent to nucleus (TEM) × 2500.
The Supplementary Material for the article entitled "Comparative analysis of global transcriptomes in nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after infecting human intestinal epithelium in vitro"
<p>The Supplementary Material (Additional files 1-5, including Table S1-S4 and Figure S1) for this article.</p> <p> </p> <p><strong>Table S1.</strong> Upregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S2.</strong> Downregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S3. </strong>The enriched GO terms in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S4. </strong>The enriched KEGG pathways in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Figure S1. </strong>The enriched GO terms and KEGG pathways in Group B relative to Group A. Bar charts show the enriched GO terms (A) and the enriched KEGG pathways (B) by significance power. Color of bars indicate power of significance and length in x axes of bar indicate number of annotated genes in the particular term of pathway. Cnetplots show the relationship between GO term (C) and KEGG pathways (D). Dot size representing GO terms and KEGG pathways indicates number of significantly changed and its annotated genes. The GO terms or KEGG pathways connected through their common and annotated genes. </p>
Figure 2 in Histomorphometrical study of the tongue epithelium of the peregrine falcon (Falco peregrinus)
Figure 2. (A) Scanning electron micrograph of the dorsal surface of the lingual apex of the falcon showing that the lingual epithelium is in a carpet shape. (X,550); (B) Scanning electron micrograph of the dorsal surface of the lingual body of the falcon showing the opening of the lingual gland (arrows). (X,300); (C) Scanning electron micrograph of the dorsal surface of the lingual body of the falcon showing the small conical papillae (single arrow) and large conical papillae (double arrows). (X,27).
Figure 1. A in Histomorphometrical study of the tongue epithelium of the peregrine falcon (Falco peregrinus)
Figure 1. A. Photomicrograph of a transverse section of the lingual apex of the falcon showing the dorsal lingual epithelium (E) and lamina propria (LP). (X, 40). B. Photomicrograph of a transverse section of the lingual body of the falcon showing the dorsal lingual epithelium (E) lingual muscles (M) and paraglossum (P). (X, 40). C. Photomicrograph of a transverse section of the lingual body of the falcon showing the dorsal lingual epithelium (E), lingual muscles (M), paraglossum (P) and the lateral epithelium (arrow) (X,40). D. Photomicrograph of a transverse section of the lingual body of the falcon showing the dorsal lingual epithelium (E) lingual muscles (M), lingual glands (G) and opening of the lingual glands (arrow). (X, 40).
De novo transcriptome assembly from the killifish, Fundulus rathbuni (gill epithelium)
<p>De novo transcriptome assembly from the killifish, Fundulus rathbuni. Fish were acclimated to either brackish or fresh water then exposed to an acute brackish water challenge. Transcriptome data from gill epithelium tissue were collected. A reference transcriptome assembly was generated from all individuals then used to analyze transcriptional responses to salinity.</p>
Data from: Live imaging of SARS-CoV-2 infected airway epithelium cultures
Open the record for dataset details and reuse information.
Commensal bacteria maintain a Qa-1b-restricted unconventional CD8+ T population in gut epithelium
<p>Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8+ T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1b-restricted CD8+ T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1b-dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigens, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Interestingly, monocolonization with <em>Pediococcus pentosaceus</em>, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1b-restricted IEL landscape.</p>
Single-cell RNA sequencing reveals dysregulated cellular programs in the inflamed epithelium of Crohn's disease patients.
<p><strong>Crohn’s disease (CD) is a complex inflammatory disorder of incompletely understood molecular aetiology. We generated a large single-cell RNA sequencing dataset from the terminal ileal biopsies of two independent cohorts comprising a total of 50 CD patients and 71 healthy controls. We performed transcriptomic analyses to reveal genes, cell types and mechanisms perturbed in CD, leveraging the power of the two cohorts to confirm our findings and assess replicability. In addition to mapping widespread alterations in cytokine signalling, we provide evidence of pan-epithelial upregulation of MHC class I genes and pathways in CD. Using non-negative matrix factorization we revealed intra- and inter-cellular upregulation of expression programs such as G-protein coupled receptor signalling and interferon signalling, respectively, in CD. We observed an enrichment of CD heritability among marker genes for various activated T cell types and myeloid cells, supporting a causal role for these cell-types in CD aetiology. Comparisons between our discovery and replication cohort revealed significant variation in differential gene-expression replicability across cell types. B, T and myeloid cells showed particularly poor replicability, suggesting caution should be exercised when interpreting unreplicated differential gene-expression result in these cell types. Overall, our results provide a rich resource for identifying cell-type specific biomarkers of Crohn’s disease and identifying genes, cell types and pathways that are causally and replicably associated with disease.</strong></p>
Atropine-functionalised gold nanoparticles binding to muscarinic receptors after passage across the intestinal epithelium
<p>Gold nanoparticles have a high potential to be a treatment of diseases by their specific drug delivery properties and multivalent receptor stimulation. For the present project, spherical gold nanoparticles were synthesised and functionalised with the muscarinic receptor antagonist atropine (Au-MUDA-AT NPs). The diameter of the gold core could precisely be controlled by using different synthetic methods and reducing agents resulting in functionalised gold nanoparticles with diameters ranging from 8 to 16 nm. The ability to interact with intestinal muscarinic receptors is size-dependent. When using intestinal chloride secretion induced by the stable acetylcholine derivative, carbachol, as read-out, the strongest inhibition, i.e. the most efficient blockade of muscarinic receptors, was observed with 13 nm sized Au-MUDA-AT NPs. Functional experiments indicate that Au-MUDA-AT NPs with a diameter of 14 nm are able to pass the intestinal mucosa in a time-dependent manner after administration to the intestinal lumen. For example, luminally administered Au-MUDA-AT NPs inhibited contractions of the small intestinal longitudinal muscle layer induced by electrical stimulation of myenteric neurons. A similar inhibition of basolateral epithelial receptors was observed after luminal administration of Au-MUDA-AT NPs when using carbachol-induced chloride secretion across the intestinal epithelium as a test system. Thus, Au-MUDA-AT NPs might be a therapeutic tool for the modulation of intestinal secretion and motility after oral application in the future.</p>
Systematic discovery of subcellular RNA patterns in the gut epithelium - Mass spectrometry data
<p>This collection contains the raw data created from the mass spectrometry experiment and the spectral counts that were used in the manuscript for protein abundance comparisons.</p>
Expression quantification from the killifish, Fundulus rathbuni (gill epithelium)
<p>Files created with the salmon quantification tool using the reference de novo transcriptome assembly from the killifish, Fundulus rathbuni.</p> <p>Fish were acclimated to either brackish or fresh water then exposed to an acute brackish water challenge. Transcriptome data from gill epithelium tissue were collected. A reference transcriptome assembly was generated from all individuals then used to analyze transcriptional responses to salinity.</p>
Intra-cellular polarization of RNAs and proteins in the human intestinal epithelium
<p>We preformed laser capture microdissection on human and mouse epithelial apical and basal compartments from the villus bottom and top followed by RNAseq. Human samples also undergone proteomics mass-spectrometry.</p>
Parameter estimation data repository - "Spatial discordances between mRNAs and proteins in the intestinal epithelium"
<p>The repository contains data associated with the estimation of protein translation and decay rates in the manuscript "Spatial discordances between mRNAs and proteins in the intestinal epithelium". Specifically, it includes MCMC-chains approximating the posterior parameter distribution and figures showing the model's fit to the data for each gene as well as a summary table of all fit results for two different models, the constant translation-rate model ("constant_rate_model") and the declining translation-rate model ("declining_rate_model") as explained in the manuscript.</p> <p>Code associated with the parameter estimation is available at https://github.com/LiBuchauer/spatial_MP_discordances .</p>
Data for: Invasive investigation: Uptake and transport of L-leucine in the gill epithelium of crustaceans
<p><span>Many aquatic species are well-known as extremely successful invaders. The green crab (<em>Carcinus</em> <em>maenas</em>) is an arthropod native to European waters; however, it is now known to be a globally invasive species. Recently it was discovered that <em>C. maenas</em> could transport nutrients in the form of amino acids across their gill from the surrounding environment, a feat previously thought to be impossible in arthropods. We compared the ability for branchial amino acid transport of crustaceans native to Canadian Pacific waters to that of the invasive <em>C. maenas</em>, determining if this was a novel pathway in an extremely successful invasive species or a shared trait among crustaceans. Active transport of L-leucine was exhibited in C<em>arcinus maenas, Metacarcinus gracilis, Metacarcinus magister</em>, and <em>Cancer</em> <em>productus</em> across their gill epithelia. <em>C. maenas</em> exhibited the highest maximum rate of branchial L-leucine transport at 53.7 ± 6.24 </span>nmolg<sup>-1</sup>h<sup>-1</sup>, over twice the rate of two native Canadian crustaceans<span>. We also examined the influence of feeding, gill specificity, and organ accumulation of L-leucine. Feeding events displayed a heavy influence on the branchial transport rate of amino acids, increasing L-leucine transport rates by up to 10-fold in <em>C. maenas</em>. L-leucine displayed </span>a significantly higher accumulation rate <span>in the gills of <em>C. maenas</em> </span>compared to the rest of the body <span>at </span>4.15 <span>± 0.78 </span>nmolg<sup>-1</sup>h<sup>-1</sup>, with the stomach, hepatopancreas, eyestalks, muscle tissue, carapace, and heart muscle exhibiting accumulation under 0.15 nmolg<sup>-1</sup>h<sup>-1</sup>. <span>For the first time, the novel transport of amino acids in Canadian native arthropods is described, suggesting that branchial amino acid transport is a shared trait among arthropods, contrary to existing literature. Further investigation is required to determine the influence of environmental temperature and salinity on transport in each species to outline any competitive advantages of the invasive <em>C. maenas</em> in a fluctuating estuarine environment. </span></p>
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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.