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111,247 results for “cells”
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 07
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 07 comprises an image series of 318 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 8 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 06
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 06 comprises an image series of 215 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 01
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 01 comprises an image series of 276 images recorded of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 4 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
NED data for the paper Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts
<p>This data repository contains NED data from the paper, <em><a href="https://arxiv.org/abs/2309.01812">Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts.</a></em></p> <p>Additional data for the NER classification task can be found here: <a href="../records/10050681">zenodo</a></p> <p> </p> <p> </p>
Interfacial host–guest complexation for inverted perovskite solar cells
<p><span>Characterisation dataset for “Interfacial host–guest complexation for inverted perovskite solar cells</span><span>”</span><span>, doi:10.1063/5.0202163, including data for main and supporting figures provided as image (*.png, *.tiff, and *.svg), Origin (*.opju) and *.txt files. </span><span>NMR data is provided by the TopSpin software, which is available from Bruker.<span> </span></span></p>
Supplementary data to "High-Resolution Raman Imaging of >300 Patient-Derived Cells from Nine Different Leukemia Subtypes: A Global Clustering Approach"
<p>Compressed ".feather" files including the entire dataset of 319 Raman maps of the same number of cells from 19 patients affected by nine distinct leukemia subtypes.<br>Raw data have been pre-processed as follows using custom software (LabVIEW, National Instruments Corp., TX): a) cosmic rays removal by singular value decomposition (SVD); b) camera offset subtraction; c) CCD response correction (intensity and etaloning) using a tungsten halogen light with known emission (Avalight-HAL, Avantes BV, NL)); d) wavenumber calibration using the zero-wavenumber laser line, toluene and argon-mercury emission (CAL-2000, Ocean Optics, Germany); e) denoising by SVD.<br>More details in the open access published article and supplementary material (10.1021/acs.analchem.4c00787).</p>
Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling in Drosophila
<p>The atypical cadherins Fat and Dachsous (Ds) signal through the Hippo pathway to regulate growth of numerous organs, including the <em>Drosophila</em> wing. Here, we find that Ds-Fat signaling tunes a unique feature of cell proliferation found to control the rate of wing growth. The duration of the cell cycle increases in direct proportion to the size of the wing, leading to linear rather than exponential growth. Ds-Fat signaling enhances the rate at which the cell cycle lengthens with wing size, thus diminishing the linear rate of wing growth. We show that this results in a complex but stereotyped relative scaling of wing growth with body growth in <em>Drosophila</em>. Finally, we examine the dynamics of Fat and Ds protein distribution in the wing, observing graded distributions that change during growth. However, the significance of these dynamics is unclear since perturbations in expression have negligible impact on wing growth.</p>
Antigen-specific memory NK cell responses against HIV and influenza utilize the NKG2/HLA-E axis
<p>For over a decade, multiple studies have disputed the notion of natural killer (NK) cells as purely innate lymphocytes by demonstrating that they are capable of putative antigen-specific immunological memory against multiple infectious agents including two critical global health priorities – human immunodeficiency virus (HIV) and influenza. However, the mechanisms underlying antigen specificity remain unknown. Herein, we demonstrate that antigen-specific human NK cell memory develops upon exposure to both HIV and influenza, unified by a conserved and epitope-specific targetable mechanism largely dependent on the activating CD94/NKG2C receptor and its ligand HLA-E, and confirm these findings by three rigorous assays. We validated the permanent acquisition of antigen-specificity by individual memory NK cells by single-cell cloning. We identified biomarkers of antigen-specific NK cell memory through complex immunophenotyping by 30-parameter flow cytometry showing elevated expression of KLRG1, a4b7, and NKG2C. Finally, we show individual HLA-E-restricted peptides that may constitute the dominant NK cell response in HIV-1- and influenza-infected persons in vivo. Our findings clarify the mechanisms behind antigen-specific memory NK cell responses, and suggest they could be targeted for future vaccines, cure strategies, or other therapeutic interventions.</p>
Data S6. Cell Size Validation Dataset
<p>This dataset contains the input values to compute the 2010 MTI in different cell sizes options, and the final MTI values. </p>
April 7, 2024 (v1) Image Open Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 5 relative to Figure 7 - Figure Supplement 4
<p>Source data file relative to <strong><span>Figure 7 – figure supplement 4 Panel A</span></strong></p> <p><span>Raw image of agarose gel showing the 2 alternative mRNAs encoding for ArhGEF11 in control animals (left track, control) and after injection of the MO at the one cell stage (right track, +MO at 2 and 5ng). The source data includes the raw files (native format .scn and open source format .tiff) as well as a pdf file showing both the full scale image and the cropped image selected for the figure.<br></span></p>
Processing of 10X 500 PBMC single cell ATAC-seq data with SnapATAC2
<p>Input files for SnapATAC2 tutorial on Galaxy</p>
General dataset of PNAS article " Ca2+ permeation through C-terminal cleaved, but not full-length human Pannexin1 hemichannels, mediates cell death"
<p>This repository contains an extended version of all real-time dye uptake evaluations, Ca2+ signal measurements, microscopic and gel images, and the corresponding statistical analyzes for each graph presented in the associated article.</p>
Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing
<p><strong>Abstract:</strong> The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.</p> <p><strong>This data sets contains:</strong></p> <p><strong>Tab. S1</strong> - Significant genes results</p> <p><strong>Tab. S2</strong> - Enriched pathways_GO_Biological Processes</p> <p><strong>Tab. S3</strong> - Enriched pathways_GO_Cellular Components</p> <p><strong>Tab. S4</strong> - Enriched pathways_GO_Molecular Function</p> <p><strong>Tab. S5</strong> - Enriched pathways_KEGG</p> <p><strong>Tab. S6</strong> - EnrichEnriched pathways_Panther</p> <p><strong>Tab. S7</strong> - Enriched pathways_Reactome</p> <p><strong>Tab. S8</strong> - Gene counts</p> <p><strong>Tab. S9</strong> - Gene selection for targeted analysis</p>
KIR2DL2/DL3+NKs and Helios+Tregs in peripheral blood predict nivolumab response in patients with metastatic renal cell cancer
<p><strong><span>Purpose</span></strong><span>: T<span>o identify predictive factors of nivolumab sensitivity, peripheral blood NKs and Tregs were evaluated </span>in patients with metastatic renal cancer (mRCC) enrolled in the REVOLUTION trial.</span></p> <p><strong><span>Experimental design:</span></strong><span> 57 mRCCs being treated with nivolumab, as at least second-line of therapy (REV), and 62 healthy donors (HDs) were longitudinally evaluated (</span><span>0-1-3-6-12 months</span><span>) for</span><span> peripheral NKs and Tregs, phenotype and function. </span><span>Multivariable logistic regression were conducted to identify the independent predictors. The </span><span>.632+ internal cross-validation was used to avoid overfitting. </span><span>The best cut-off value </span><span>based on three-months clinical-response</span><span> was applied to </span><span>progression-free survival (PFS)</span><span> and </span><span>overall survival (OS)</span><span>. Kaplan-Meier curves for PFS and OS were produced.</span></p> <p><strong><span>Results:</span></strong><span> </span><span>At pre-treatment, mRCCs displayed high frequency of <sup>NKp46+</sup>NKs, <sup>NKp30+</sup>NKs, <sup>KIR2DL1+</sup>NKs, <sup>KIR2DL2/DL3+</sup>NKs, and<sup> PD-1+</sup>NKs with reduced NK degranulation; as well as high frequency of Tregs, </span><sup><span>PD-1+</span></sup><span>Tregs,</span><sup><span> Helios+</span></sup><span>Tregs and </span><sup><span>ENTPD-1+</span></sup><span>Tregs</span><span>. Responder patients (R), identified as a clinical response after three-months of treatment,</span><span> presented at pre-treatment significantly low CD3<sup>+</sup>, high<sup> KIR2DL2/DL3+</sup></span><span>NKs</span><span>, high <sup>PD-1+</sup>Tregs and high <sup>Helios+</sup>Tregs. Upon multivariate analysis, only <sup>KIR2DL2/DL3</sup>NKs and <sup>Helios+</sup>Tregs held as independent predictors of nivolumab responsiveness. The <sup>KIR2DL2/DL3+</sup>NKs >35.3% identified patients with longer OS while the <sup>Helios+</sup>Tregs >34.3% displayed significantly longer PFS. After 1-month of nivolumab, R patients showed low CD3<sup>+</sup>, high NKs, <sup>KIR2DL2/DL3+</sup>NKs and <sup>ICOS+</sup>Tregs. Among these subpopulations, CD3<sup>+</sup> and <sup>KIR2DL2/DL3+</sup>NKs held as independent predictors of nivolumab efficacy. Low CD3<sup>+ </sup>(≤71%) significantly associated with longer PFS while high <sup>KIR2DL2/DL3+</sup>NKs (>23.3%) associated with both PFS and OS. </span></p> <p><strong><span>Conclusions:</span></strong><span> Pre-treatment evaluation of <sup>Helios+</sup>Tregs/<sup>KIR2DL2/DL3+</sup>NKs and one-month post-treatment CD3<sup>+</sup>/<sup> KIR2DL2/DL3+</sup>NKs will predict nivolumab response in mRCCs<span>.</span></span></p>
cell-niches
Open the record for dataset details and reuse information.
FLAIR2 results from LRGASP R2C2 sequencing of Human WTC11 and Mouse ES cell lines
<p>FLAIR2 results from Oxford Nanopore sequencing of R2C2 libraries generated from Human WTC11 and Mouse ES cell lines from the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) (Pardo-Palacios et al. Nature Methods 2024). FLAIR2 high-confidence isoforms are provided for WTC11 and ES cells. For Mouse ES cells, sequence variants were identified with Longshot and incorporated into transcript isoforms using FLAIR2. These data are associated with the FLAIR2 publication (Tang et al. 2024)</p>
Evolution of plasma properties in 2D particle-in-cell simulations of pulsar polar caps as function of dipole inclination angle
<p>The video shows the evolution of plasma properties in polar cap region of neutron stars from initial simulation conditions to the quasi-periodic pair creation. Three inclination angles of magnetic dipole axis to the star rotation axis are investigate \iota = 0°, 45°, and 90°.</p> <p>The presented quantities are (in rows): Parallel current density, parallel electric field, parallel and perpendicular Poynting flux, electron and positron plasma density, and electron and positron plasma bulk momenta.</p> <p> </p>
CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues
<p>Cis-regulatory elements (CREs) play a pivotal role in gene expression regulation, allowing cells to serve diverse functions and respond to external stimuli. To address this gap, we have created CREdb, a comprehensive database of over 10 million human regulatory elements across 1,058 cell types and 315 tissues. Data from 11 sources were curated and mapped to standard ontological terms. 11,223,434 combined elements are present in the final database, and these were merged into 5,666,240 consensus elements representing the combined ranges of the individual elements informed by their overlap. Each consensus element contains metadata including the number of elements supporting it and a hash linking to the source databases. The inferred activity of each consensus element in various cell-type and tissue context is also provided.</p>
Data files for "Mitochondria-enriched protrusions are associated with brain and intestinal stem cells in Drosophila"
<p>This entry is for our report "Mitochondria-enriched protrusions are associated with brain and intestinal stem cells in <em>Drosophila" </em>by Sharyn A. Endow, Sara E. Miller & Phuong Thao Ly in <em>Commun Biol </em><strong>2</strong>, 427 (2019). <a href="https://doi.org/10.1038/s42003-019-0671-4">https://doi.org/10.1038/s42003-019-0671-4</a></p> <p>The deposited datasets contain the 1) EM raw images, 2) immunofluorescence microscopy (IFM) raw images, 3) live imaging raw sequences, and 4) data analysis files.</p>
HAEOLUS Project Fuel Cell Data.
<p>Dataset from a Fuel Cell test in the HAEOLUS European Project <a href="https://haeolus.eu/" target="_blank" rel="noopener">https://haeolus.eu/.</a></p> <p> </p>
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.