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111,247 results for “cells”
Dataset used for "Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data"
<p>Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically. </p>
Multi-Electrode Array with a Planar Surface for Cell Patterning by Microprinting_experimental dataset
<p>This file contains the raw unprocessed experimental data for the results published in Slavík et al., Multi-Electrode Array with a Planar Surface for Cell Patterning by Microprinting, Sensors 2019, 19(24), 5379. </p>
TCRb repertoires of murine CD8T cells following viral infection
<p>TCRbeta repertoires from Tcf7-GFP transgenic GFP mice were FACS isolated and sequenced following viral infection. </p>
Data from: Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells
<p>CSV files of whole-Genome Knockout Screens for Proliferation and Tumorigenic Growth. The data is retrieved from:</p> <p>Title: "Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells"</p> <p>DOI: https://doi.org/10.1016/j.celrep.2020.03.029</p> <p>The excel sheet with data shown in figure 1B is converted to CSV files.</p>
Simulation dataset of "Particle-in-cell simulations of characteristics of rising-tone chorus waves in the inner magnetosphere"
<p>Simulation dataset of "Particle-in-cell simulations of characteristics of rising-tone chorus waves in the inner magnetosphere", including magnetic fields and parallel and perpendicular temperatures of energetic electrons.</p>
Data from: Single cell RNA-seq analysis reveals that prenatal arsenic exposure results in long-term, adverse effects on immune gene expression in response to Influenza A infection
<p>Arsenic exposure via drinking water is a serious environmental health concern. Epidemiological studies suggest a strong association between prenatal<i> </i>arsenic exposure and subsequent childhood respiratory infections, as well as morbidity from respiratory diseases in adulthood, long after systemic clearance of arsenic.<i> </i>We investigated the impact of exclusive prenatal arsenic exposure on the inflammatory immune response and respiratory health after an adult influenza A (IAV) lung infection. C57BL/6J mice were exposed to 100 ppb sodium arsenite<i> in utero,</i> and subsequently infected with IAV (H1N1) after maturation to adulthood. Assessment of lung tissue and bronchoalveolar lavage fluid (BALF) at various time points post IAV infection reveals greater lung damage and inflammation in arsenic exposed mice versus control mice. Single-cell RNA sequencing analysis of immune cells harvested from IAV infected lungs suggests that the enhanced inflammatory response is mediated by dysregulation of innate immune function of monocyte derived macrophages, neutrophils, NK cells, and alveolar macrophages. Our results suggest that prenatal arsenic exposure results in lasting effects on the adult host innate immune response to IAV infection, long after exposure to arsenic, leading to greater immunopathology. This study provides the first direct evidence that exclusive prenatal exposure to arsenic in drinking water causes predisposition to a hyperinflammatory response to IAV infection in adult mice, which is associated with significant lung damage.</p>
Accompanied data files used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis"
<p>lists of source file used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis" by Jing Yang, Amanda McGovern, Paul Martin, Kate Duffus, Xiangyu Ge, Peyman Zarrineh, Andrew P Morris, Antony Adamson, Peter Fraser, Magnus Rattray & Stephen Eyre. The paper has been accepted by Nature Communications.</p>
Experiments, drainage, 2D Hele Shaw cell
<p>Drainage experiment in a horizontal two_dimensional Hele-Shaw cell</p>
Data from: Zebrafish retinal ganglion cells asymmetrically encode spectral and temporal information across visual space
<p>In vertebrate vision, the tetrachromatic larval zebrafish permits non-invasive monitoring and manipulating of neural activity across the nervous system in vivo during ongoing behaviour. However, despite a perhaps unparalleled understanding of links between zebrafish brain circuits and visual behaviours, comparatively little is known about what their eyes send to the brain via retinal ganglion cells (RGCs). Major gaps in knowledge include any information on spectral coding, and information on potentially critical variations in RGC properties across the retinal surface corresponding with asymmetries in the statistics of natural visual space and behavioural demands. Here, we use in vivo two photon (2P) imaging during hyperspectral visual stimulation as well as photolabeling of RGCs to provide a functional and anatomical census of RGCs in larval zebrafish. We find that RGCs' functional and structural properties differ across the eye and include a notable population of UV-responsive On-sustained RGCs that are only found in the acute zone, likely to support visual prey capture of UV-bright zooplankton. Next, approximately half of RGCs display diverse forms of colour opponency including many that are driven by a pervasive and slow blue-Off system - far in excess of what would be required to satisfy traditional models of colour vision. In addition, most information on spectral contrast was intermixed with temporal information. Taken together, our results suggest that zebrafish RGCs send a diverse and highly regionalised time-colour code to the brain.</p>
The MATLAB code for "A kinematic model for understanding rain formation efficiency of a convective cell"
<p>Please check the code for the 1D model and the plotting commands. Please start from main.m </p>
Tissue-resident memory Th17 cells maintain stable fungal commensalism in the oral mucosa
<p>Raw data files linked to a manuscript published in Mucosal Immunology 2020 (accepted for publication on July 6th,.2020)</p>
Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction
<p>The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.</p>
SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections (Revision data)
<p>The submitted dataset, correspond to the RAW (*.czi format) and analysis files of the <strong>revisions</strong> of manuscript "SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections", which has been processed for revision (2020-01-31) by PLOS Biology.</p> <p>The files are in *.zip format and the naming follows thenumbering of the manuscript figures, which will be found in bioRxiv.org (<strong>ID#: BIORXIV/2020/938571</strong>). Each *.zip files contains a document with the description of all the provided files.</p>
Online supplement for "T cell costimulation blockade blunts age-related heart failure"
<p><strong>ONLINE SUPPLEMENT FOR:</strong></p> <p><strong>Research Letter:</strong></p> <p><strong>T cell costimulation blockade blunts age-related heart failure</strong></p>
Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon vaccination
<p>Data set accompanying the publication "Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon vaccination".</p> <p>In this study, we utilize high-throughput sequencing to profile the memory CD4 TCRβ repertoire and track vaccine-specific and epitope-specific TCRβ clonotypes following the de novo administration of hepatitis B (HepB) vaccine in healthy HepB-naïve individuals.</p> <p>The data set is comprised out of the following parts:</p> <ul> <li>repTCRb: Folder containing CD4+ TCR repertoire data from volunteers. Some of these samples are also available in ImmuneAccess (https://clients.adaptivebiotech.com/pub/deneuter-2018-cmvserostatus).</li> <li>peptideTCRab: Folder containing peptide-specific or peptide-pool-specific TCR data</li> <li>df_all: Meta and FC data for samples and volunteers</li> <li>freqCD154: CD154-based group definitions</li> <li>groups.csv: Group definitions used for classes</li> </ul>
Global Characterization of Megakaryocytes in Bone Marrow, Peripheral Blood, and Cord Blood by Single-cell RNA Sequencing
<p><span><span>Megakaryocytes (MK) are mainly derived from bone marrow (BM) and are mainly involved in platelet production. Recent studies have shown that MK derived from BM may have immune function, and that MK from peripheral blood (PB) are associated with prostate cancer. We analyzed more than 1.2 million single-cell transcriptome data from 132 samples of PB, BM, and cord blood (CB) from healthy individuals and patients, and obtained 4474 MK single cell and 14 MK subtypes. We found that MK were widely distributed and the amount of MK in PB was more than that in BM and there were specificity MK subtypes in PB. We found classical MK1 with typical MK characteristics and non-classical MK2 closely related to immunity which was the most common subtype in BM and CB. Classical MK1 was closely related to Non-Small Cell Lung Cancer (NSCLC) and has diagnostic ability. MK2 may have potential adaptive immune function and play a role in tumor NSCLC and autoimmune diseases Systemic Lupus Erythematosus. This study deepened our understanding of MK and suggested that MK had potential immune functions and was involved in various diseases.</span></span></p>
Comparing Lifeact and Phalloidin for super-resolution imaging of actin in fixed cells
<p>Visualizing actin filaments in fixed cells is of great interest for a variety of topics in cell biology such as cell division, cell movement, and cell signaling. We investigated the possibility of replacing phalloidin, the standard reagent for super-resolution imaging of F-actin in fixed cells, with the actin binding peptide `lifeact'. We compared the labels for use in single molecule based super-resolution microscopy, where AlexaFluor 647 labeled phalloidin was used in a (d)STORM modality and Atto 655 labeled lifeact was used in a single molecule imaging, reversible binding modality. We found that imaging with lifeact had a comparable resolution in reconstructed images and provided several advantages over phalloidin including lower costs, the ability to image multiple regions of interest on a coverslip without degradation, simplified sequential super-resolution imaging, and more continuous labeling of thin filaments.</p>
Fluorescent (C)LSM image sequences of Dictyostelium discoideum (Ax2 - LifeAct mRFP) for cell track and cell contour analysis
<p>This data set is designed for cell contour and cell track analysis. Hence image sequences of moving Dictyostelium discoideum cells are recorded. For the purpose to facilitate the detection of the cell contour we take fluorescent images of the cortical protein actin to obtain a high contrast between background and cell body. In each image sequences several cells are recorded. This allows for an analysis of all cells at once or to crop single cell tracks.</p>
FIB-tomography data of Ni-YSZ anodes for Solid Oxide Fuel Cells (SOFC): Comparison of pristine and degraded materials (before/after redox cycling)
<p><em>Contents: </em></p> <p>This dataset contains 3D image stacks acquired with FIB-tomography from Ni-YSZ cermet anodes for Solid Oxide Fuel Cells (SOFC).</p> <p>The data was collected from three different Ni-YSZ anodes (fine-, medium- and coarse-grained). Each of these anodes was investigated first in pristine state (after sintering and reduction) and then also in degraded state (after exposure to 8 redox cycles).</p> <p>The 6 tomographs are then presented as stacks of 2D-tiff-images in 2 different versions: as gray-scale images (raw data) and as segmented images (Ni=white, YSZ=gray and pores=black). In total this gives 12 image stacks.</p> <p><strong>Further details</strong>, such as the voxel resolutions and image window sizes are listed in the downloadable excel file (<strong>2_3D_Data_Info.xlsx</strong>).</p> <p> </p> <p><em>Scientific Context: </em></p> <p>The microstructures of the cermet anodes were investigated for the purpose of optimizing the anode performance, which depends on effective transport properties (i.e. conductivity of ions in YSZ and of electrons in Ni, as well as diffusivity of fuel/gas in the pores). Furthermore the anode performance also depends on the catalytic/electrochemical activity (i.e. Ni-surface area and three phase boundary length TPBL). The microstructure characteristics have a strong influence on effective properties, electrochemical activity and associated anode performance. Furthermore, microstructure degradation (e.g. by Ni-coarsening) may lead to performance loss over time.</p> <p>Hence, the investigations focus on a fundamental, quentitative understanding of the relationships between microstructure characteristics and effective properties. The study reveals quantitative descriptions of all relevant microstructure characteristics (porosity, tortuosity, constrictivity, surface/interface areas, TPBL) and of the corresponding effective transport porperties (electric and ionic.conductivities). The corresponding anode performance was characterized by impedance spectroscopy.</p> <p>The quantitative <strong>results of the microstructure investigation were published</strong> in:</p> <p><strong>Pecho et al</strong> 2015a (doi:10.3390/ma8095265),</p> <p><strong>Pecho et al</strong> 2015b (doi:10.3390/ma8105370),</p> <p><strong>Holzer et al</strong> 2013 (doi: 10.1016/j.jpowsour.2013.05.047),</p> <p><strong>Holzer et al</strong> 2011a (doi: 10.1016/j.jpowsour.2010.08.017) and</p> <p><strong>Holzer et al</strong> 2011b (doi: 10.1016/j.jpowsour.2010.08.006).</p>
Comparing the effect of TGF-β receptor inhibition on human mesenchymal stem/stromal cells derived from endometrium, bone marrow and adipose tissues
<p><strong>Figure S1: Differences between bmMSC donors. A)</strong> Graph showing two groups of bmMSCs with and without effect of A83-01 treatment on % SUSD2<sup>+</sup> cells. <strong>B)</strong> Graph showing no difference in the number of cells following A83-01 treatment in the two groups of donor cells from <strong>A</strong>. Plots are median for n=3 biological samples per treatment group.</p>
ScienceDex guides
Understand access before you commit
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.