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111,247 results for “cells”
Dataset for: "Parameter identifiability and model selection for partial differential equation models of cell invasion"
<p>This is the dataset accompanying the paper "Parameter identifiability and model selection for partial differential equation models of cell invasion" (https://arxiv.org/abs/2309.01476). It consists of a series of images taken of a barrier assay experiment to study tissue expansion of MDCK cells, along with cell density data in MATLAB format.</p> <p>File structure: the contents of the four zip files should be combined (they were split into four files for practical reasons regarding file size). The data corresponds to eight experiments, four with circular initial conditions, and four with triangular initial conditions, the associated data are located in 04-05-22 exp1/Circle and 04-05-22 exp1/Triangle respectively, each labeled "xy<n>", where <n> from 1 to 8 is an identifier for the experiment. The images under the xy<n>_Phase folders are the raw images taken of the experiment, those under the xy<n>_mask folder are processed images indicating the extend of the spread of the cell population. The DensityCellcyleFraction folder contain data files in MATLAB format. The most relevant is the "density" variable, which is a rank-3 tensor of size 150x150x77 such that density(i,j,k) corresponds to the cell density at location (x_i,y_j) and time t_k. The process for calculating the cell density is described in the paper.</p> <p>Alternatively, the density data is also provided in csv format. In the csv_data folder, xy<n>/t<k>.csv encodes a matrix representing cell density for experiment <n> at time t_k.</p> <p>The code for processing and analysing these data are provided in the "code" folder. It is also available at https://github.com/liuyue002/woundhealing .</p> <p>Abstract of the paper:</p> <p>When employing a mechanistic model to study biological systems, practical parameter identifiability is important for making predictions in a wide range of scenarios, as well as for understanding the mechanisms driving the system behaviour. We argue that parameter identifiability should be considered alongside goodness-of-fit and model complexity as criteria for model selection. To demonstrate, we use a profile likelihood approach to investigate parameter identifiability for four extensions of the Fisher--KPP model, given experimental data from a cell invasion assay. We show that more complicated models tend to be less identifiable, with parameter estimates being more sensitive to subtle differences in experimental procedures, and require more data to be practically identifiable. The results from identifiability analysis can inform model selection, as well as data collection and experimental design.</p>
Data archive for: Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions
<p>Data archive for: “Resting cells of <em>Skeletonema marinoi</em> assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions” <a href="https://doi.org/10.1111/1462-2920.16625">https://doi.org/10.1111/1462-2920.16625</a></p> <p> </p> <p>Dataset of single cell assimilation of organic/inorganic C/N by resting cells of the marine diatom <em>Skeletonema marinoi</em> captured using secondary ion mass spectrometry (SIMS) and stable isotopic tracers. The dataset also contains POC/PON changes over time during dormancy, DNRA (<sup>15</sup>N-NH<sub>4</sub><sup>+</sup> production), denitrification (<sup>15</sup>N-N<sub>2</sub> production) and a germination assay to determine survival rate, most probable number analysis (MPN). </p> <p>Two strains (GF04 and R05) were incubated in dark and anoxic conditions in two different incubation experiments.</p> <p>Incubation 1: Diatoms treated with antibiotics before entering dormancy compared to a control not treated with antibiotics then given <sup>15</sup>N-NO<sub>3</sub><sup>-</sup> in dark anoxic conditions.</p> <p>Incubation 2: Diatoms treated with antibiotics given, <sup>15</sup>N & <sup>13</sup>C urea, <sup>15</sup>N & <sup>13</sup>C urea + <sup>14</sup>N-NO<sub>3</sub><sup>-</sup>, <sup>13</sup>C-acetate, <sup>13</sup>C-acetate + <sup>15</sup>N-NO<sub>3</sub><sup>-</sup>, or <sup>15</sup>N-NO<sub>3</sub><sup>-</sup>.</p> <p>See the main manuscript for a extensive experimental setup.</p> <p> </p> <p><strong>Each file is uploaded as both a .CSV and .XLSX, so that you can choose which you prefer.</strong></p> <p><strong>DNRA_and_denitrification.csv/xlsx:</strong> DRNA and denitrification depending on volume (Incubation 1)</p> <p><strong>DNRA_per_cell.csv/xlsx:</strong> DNRA per cell (Incubation 1 & 2)</p> <p><strong>MPN_data.csv/xlsx:</strong> Most probable number analysis (Incubation 1 & 2)</p> <p><strong>POC_PON.csv/xlsx:</strong> POC and PON per cell and volume (Incubation 1 & 2)</p> <p><strong>SIMS_data.csv/xlsx:</strong> SIMS data (Incubation 1 & 2)</p> <p> </p> <p> </p>
Discrete Flow Cytometry of Underway Samples from TN427 Using a BD Influx Cell Sorter
<p>The dataset consists of BD Influx-based analysis of phytoplankton populations from discrete flow cytometry data collected underway during the University of Washington School of Oceanography 2024 undergraduate senior thesis research cruise (TN427) from American Samoa. The data consists of cell abundance, cell size (equivalent spherical diameter), carbon quota, and carbon biomass for picophytoplankton populations, namely the cyanobacteria Prochlorococcus and Synechococcus, and small eukaryotic phytoplankton (<5 μm ESD). Time is in UTC format, latitude and longitude are in decimal degrees, and depth is in meters. Further information can be found here: [https://github.com/fribalet/FCSplankton](https://github.com/fribalet/FCSplankton)</p>
Single-cell RNA-seq profiles of lung adenocarcinoma patients and tumor-bearing mice
<p>single-cell RNA sequencing (scRNA-seq) profiles from eight patients with lung adenocarcinoma (LUAD) and four samples of tumor tissues from tumor bearing mice were performed. By integrating other scRNA-seq data and clinical information, we identified activated adaptive immune responses in older patients, reflected by enriched dysfunctional T cell signature scores and immune checkpoint molecules. Our study shows increased efficacy of immune checkpoint blockade therapy in older patients, addressing the prominent role of age when considering immunotherapy.</p>
Genetic architecture of immune cell DNA methylation in the rhesus macaque
<p><strong>Complete model outputs from rhesus macaque (<em>Macaca mulatta</em>) whole blood meQTL and eQTL analyses in article, "Genetic architecture of immune cell DNA methylation in the rhesus macaque". </strong></p> <p><strong><em>cis</em> meQTL model output (SNP-CpG associations):</strong> </p> <ol> <li>IMAGE_573_meqtl_model_res_wPVE.txt: <ul> <li>Model results from IMAGE meQTL mapping including all genome, chromatin state annotations, and PVE estimates</li> </ul> </li> <li>pqlseq_allimagesnps_res_converged_wpve.txt: <ul> <li>Model results from PQLseq meQTL mapping including PVE estimates </li> </ul> </li> </ol> <p><strong><em>cis</em> eQTL model output (SNP-gene associations): </strong></p> <ol> <li>eqtl_res_sva5_gemma_172samples_qvalue.txt: <ul> <li>Model results from GEMMA eQTL mapping </li> </ul> </li> </ol> <p> </p>
Data from: A eudicot MIXTA family ancestor likely functioned in both conical cells and trichomes
<p>The <em>MIXTA</em> family of MYB transcription factors modulate the development of diverse epidermal features in land plants. This study investigates the evolutionary history and function of the <em>MIXTA </em>gene family in the early-diverging eudicot model lineage <em>Thalictrum </em>(Ranunculaceae), with R2R3 SBG9-A MYB transcription factors representative of the pre core-eudicot duplication and thus hereby referred to as "paleo<em>MIXTA</em>" (<em>PMX</em>).</p> <p>Cloning and phylogenetic analysis of <em>Thalictrum paleoMIXTA</em> (<em>ThPMX</em>) orthologs across 23 species reveals a genus-wide duplication coincident with a Whole Genome Duplication. Expression analysis by qPCR confirmed the highest expression is found in carpels, while newly revealing high expression in leaves and nuanced differences between paralogs in representative polyploid species. The single copy ortholog from the diploid species <em>T. thalictroides </em>(<em>TthPMX</em>, previously <em>TtMYBML2</em>),<em> </em>which has petaloid sepals with conical papillate cells and trichomes on leaves, was functionally characterized by virus induced gene silencing (VIGS) and its role in leaves was also assessed from heterologous over-expression in tobacco. Another ortholog from a species with conical papillate cells on stamen filaments, <em>TclPMX</em>, was also targeted for silencing. Overexpression assays in tobacco provide further evidence that the <em>paleoMIXTA</em> lineage has the potential for leaf trichome function in a core eudicot. Transcriptome analysis by RNA-Seq on leaves of VIGS-treated plants suggests<em> </em>that <em>TthPMX </em>modulates<em> </em>leaf trichome development and morphogenesis through microtubule-associated mechanisms and that this may be a conserved pathway for eudicots. These experiments provide evidence for a combined role for <em>paleoMIXTA</em> orthologs in (leaf) trichomes and (floral) conical papillate cells that, together with data from other systems, makes the functional reconstruction of a eudicot ancestor most likely as also having a combined function.</p>
Multi-cell type deconvolution using a probabilistic model for single-molecule DNA methylation haplotypes
<p>Files required to run deconvolution with CelFIE-ISH and Epistate, in U250 regions from Loyfer et al. 2023, in both "pat" and "epiread" formats. </p>
Automatic monitoring of neural activity with single-cell resolution in behaving Hydra
<p>The ability to record every spike from every neuron in a behaving animal is one of the holy grails of neuroscience. Here, we report coming one step closer towards this goal with the development of an end-to-end pipeline that automatically tracks and extracts calcium signals from individual neurons in the cnidarian <em>Hydra vulgaris</em>. We imaged dually labeled (nuclear tdTomato and cytoplasmic GCaMP7s) transgenic <em>Hydra </em>and developed an open-source Python platform (TraSE-IN) for the Tracking and Spike Estimation of Individual Neurons in the animal during behavior. The TraSE-IN platform comprises a series of modules that segments and tracks each nucleus over time and extracts the corresponding calcium activity in the GCaMP channel. Another series of signal processing modules allows robust prediction of individual spikes from each neuron's calcium signal. This complete pipeline will facilitate the automatic generation and analysis of large-scale datasets of single-cell resolution neural activity in <em>Hydra</em>, and potentially other model organisms, paving the way towards deciphering the neural code of an entire animal.</p>
Cross-reactive CD8+ T cell responses to tumor-associated antigens (TAAs) and homologous microbiota-derived antigens (MoAs)
<p><strong><span>Background: </span></strong><span>We have recently shown extensive sequence and conformational homology between tumor-associated antigens (TAAs) and antigens derived from microorganisms (MoAs). The present study aimed to assess the breadth of T-cell recognition specific to MoAs and the corresponding TAAs in healthy subjects (HS) and patients with cancer (CP).</span></p> <p><strong><span>Method: </span></strong><span>A library of >100 peptide-MHC (pMHC) combinations was used to generate DNA-barcode labelled multimers. Homologous peptides were selected from the Cancer Antigenic Peptide Database, as well as Bacteroidetes/Firmicutes-derived peptides. They were incubated with CD8+ T cells from the peripheral blood of HLA-A*02:01 healthy individuals (n=10) and cancer patients (n=16). T cell recognition was identified using tetramer-staining analysis. Cytotoxicity assay was performed using as target cells TAP-deficient T2 cells loaded with MoA or the paired TuA.</span></p> <p><strong><span>Results: </span></strong><span>A total of 66 unique pMHC recognized by CD8+ T cells across all groups were identified. Of these, 21 epitopes from microbiota were identified as novel immunological targets. Reactivity against selected TAAs was observed for both HS and CP. pMHC tetramer staining confirmed CD8+ T cell populations cross-reacting with CTA SSX2 and paired microbiota epitopes. Moreover, PBMCs activated with the MoA where shown to release IFNγ as well as to exert cytotoxic activity against cells presenting the paired TuA.</span></p> <p><strong><span>Conclusions: </span></strong><span>Several predicted microbiota-derived MoAs are recognized by T cells in HS and CP. Reactivity against TAAs was observed also in HS, primed by the homologous bacterial antigens. CD8+ T cells cross-reacting with MAGE-A1 and paired microbiota epitopes were identified in three subjects. Therefore, the microbiota can elicit an extensive repertoire of natural memory T cells to TAAs, possibly able to control tumor growth (“natural anti-cancer vaccination”). In addition, non-self MoAs can be included in preventive/therapeutic off-the-shelf cancer vaccines with more potent anti-tumor efficacy than those based on TAAs.</span></p>
Gene embeddings used in GenePT: A Simple But Hard-to-Beat Foundation Model for Genes and Cells Built From ChatGPT
<p>These are the pulled NCBI (and UniProt, when applicable) summaries of genes, as well as the corresponding OpenAI text embeddings (text-embedding-ada-002 and text-embedding-3-large) computed on the summaries. See methods details in Chen and Zou (2024+).</p> <p>The unzipped folder contains four different files: </p> <ol> <li>NCBI_summary_of_genes.json (NCBI gene card summary of human genes)</li> <li>NCBI_UniProt_summary_of_genes.json (NCBI gene card and UniProt protein (when applicable) summary of human genes)</li> <li>GenePT_gene_embedding_ada_text.pickle (a dictionary of numpy array where gene names (upper case) are keys and text-embedding-ada-002 embeddings of the summary in 1. are the values)</li> <li>GenePT_gene_protein_embedding_model_3_text.pickle (a dictionary of numpy array where gene names (upper case) are keys and text-embedding-3-large embeddings of the summary in 1. are the values)</li> </ol> <p>Reference:</p> <p>Chen YT, Zou J. (2024+) GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT. bioRxiv preprint: <a href="https://www.biorxiv.org/content/10.1101/2023.10.16.562533v1">https://www.biorxiv.org/content/10.1101/2023.10.16.562533v1</a>.</p>
Fig.ç6.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 1 and 2, ventral view; B, segments 4 and 5, ventral view. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; lvt, lateroventral tubule; pac, pachycyclus; pf, pectinate fringe; rss, rounded sensory spot. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç6.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 1 and 2, ventral view; B, segments 4 and 5, ventral view. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; lvt, lateroventral tubule; pac, pachycyclus; pf, pectinate fringe; rss, rounded sensory spot.
Fig.ç5.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 1 and 2, dorsal view; B, segment 4, dorsal view. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; mds, middorsal spine; pac, pachycyclus; pf, pectinate fringe; ps, perforation site; rss, rounded sensory spot. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç5.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 1 and 2, dorsal view; B, segment 4, dorsal view. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; mds, middorsal spine; pac, pachycyclus; pf, pectinate fringe; ps, perforation site; rss, rounded sensory spot.
Fig.ç7.Ec hinoderes ohtsukai sp. nov., paratype, female (ZIHU 3980), Nomarski photomicrographs. A, Segments 5 and 6, ventral view; B, segments 8 and 9, ventral view. Abbreviations: dss, droplet-shaped sensory spot; gco2, modi ed glandular cell outlet type II; lvt, lateroventral tubule; si, sieve plate; sp, sternal plate; tp, tergal plate. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç7.Ec hinoderes ohtsukai sp. nov., paratype, female (ZIHU 3980), Nomarski photomicrographs. A, Segments 5 and 6, ventral view; B, segments 8 and 9, ventral view. Abbreviations: dss, droplet-shaped sensory spot; gco2, modi ed glandular cell outlet type II; lvt, lateroventral tubule; si, sieve plate; sp, sternal plate; tp, tergal plate.
Fig.ç3.Ec hinoderes ohtsukai sp. nov., scanning electron micrographs. A, B, Paratype, female (ZIHU 3983); C–E, paratype, male (ZIHU 3982). A, General habitus, lateral view; B, neck and segments 1–4, lateral view; C, enlargement of segment 7, lateral view; D, enlargement of segment 9, lateral view; E, enlargement of segments 10 and 11, lateroventral view. Abbreviations: ch, cuticular hair; dss, droplet-shaped sensory spot; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; pf, pectinate fringe; po, pore; ps1, penile spine 1; ps2, penile spine 2; ps3, penile spine 3; rss, rounded sensory spot; si, sieve plate; ss, sensory spot. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç3.Ec hinoderes ohtsukai sp. nov., scanning electron micrographs. A, B, Paratype, female (ZIHU 3983); C–E, paratype, male (ZIHU 3982). A, General habitus, lateral view; B, neck and segments 1–4, lateral view; C, enlargement of segment 7, lateral view; D, enlargement of segment 9, lateral view; E, enlargement of segments 10 and 11, lateroventral view. Abbreviations: ch, cuticular hair; dss, droplet-shaped sensory spot; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; pf, pectinate fringe; po, pore; ps1, penile spine 1; ps2, penile spine 2; ps3, penile spine 3; rss, rounded sensory spot; si, sieve plate; ss, sensory spot.
Fig.ç2.Ec hinoderes ohtsukai sp. nov., camera lucida drawings. A, B, Holotype, male (ZIHU 3976), entire animal, dorsal and ventral view, respectively; C, D, allotype, female (ZIHU 3977), segments 9–11, dorsal and ventral view, respectively. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; lts, lateral terminal spine; lvt, lateroventral tubule; mds, middorsal spine; ne, neck; ps, penile spine; rss, rounded sensory spot; si, sieve plate. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç2.Ec hinoderes ohtsukai sp. nov., camera lucida drawings. A, B, Holotype, male (ZIHU 3976), entire animal, dorsal and ventral view, respectively; C, D, allotype, female (ZIHU 3977), segments 9–11, dorsal and ventral view, respectively. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; lts, lateral terminal spine; lvt, lateroventral tubule; mds, middorsal spine; ne, neck; ps, penile spine; rss, rounded sensory spot; si, sieve plate.
ERK signaling of invasive cells in mammary organoid
<p>Live-cell imaging of HMT3522 T4-2 invasive mammary epithelial cell line, with fluorescent ERKTR cell signaling reporter and nuclear reporter, to extract trajectory pairs of ERKTR to nuclear cross-correlation as a measure of ERK signaling activity. Datasets X and Y capture ERK signaling state at t and t+1 respectively, while test_obs contains test trajectories and inds_test_starts contains the indices of starting times of test trajectories.</p>
Accompanying dataset for: "IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues"
<p>Mouse datasets were acquired using the manual IBEX multiplex imaging protocol and accompany the manuscript “IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues”, A. Radtke <em>et al.</em>, 2020, PNAS.</p> <p>All image data are stored using the <a href="https://imaris.oxinst.com/support/imaris-file-format">Imaris file format</a>. To view these multi-channel images, you can either use one of these free viewers, <a href="https://imaris.oxinst.com/imaris-viewer">Imaris viewer</a>, <a href="https://imagej.net/Fiji">Fiji</a>.</p> <p>Each experiment has an associated imaging meta-data file in xlsx format and the resulting image in Imaris format.</p> <p><strong>Mouse spleen (Manual)</strong></p> <p>Dataset is a 16 parameter IBEX experiment performed on a mouse spleen section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse thymus (Manual)</strong></p> <p>Dataset is a 26 parameter IBEX experiment performed on a mouse thymus section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse lung (Manual)</strong></p> <p>Dataset is a 23 parameter IBEX experiment performed on a mouse lung section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.379 µm), y (0.379 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse small intestine (Manual)</strong></p> <p>Dataset is a 20 parameter IBEX experiment performed on a mouse small intestine section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse liver (Manual)</strong></p> <p>Dataset is an 18 parameter IBEX experiment performed on a liver section from a LysM-tdtomato reporter mouse labeled with antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse naive lymph node (Manual)</strong></p> <p>Dataset is a 41 parameter IBEX experiment performed on a mouse lymph node section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse immunized lymph node (Manual)</strong></p> <p>Dataset is a 41 parameter IBEX experiment performed on a mouse lymph node section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p>
Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue - IMC+RNAScope images
<p><span>Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides.<span> </span>We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.</span></p>
Cell Painting Dataset of EUbOPEN compounds
<p>This parquet file is a dataset of cell painting profiles generated using a technique of morphological profiling known as the Cell Painting Assay (CPA). The CPA aims at deeply characterizing modulator from their ‘fingerprint’ in human cells as seen in microscopic images.</p> <p>Cells subjected to treatments are fixed, stained and imaged. These images are analysed and more than 7500 features are extracted using a cell profiler pipeline. Single cell level profiles are aggregated into well-level profiles which can be used to compare and contrast chemical treatments. </p> <p>Morphological profiling using cell painting begins with the culture of bone sarcoma U2OS cells in control and perturbation conditions for 24 to 48 hours. These cells are then subjected to 4% PFA fixation and staining with 6 inorganic dyes (Hoechst 33342 Nuclear Stain, Concanavalin A 488, Nucleic Acid Stain, WGA 555, Phalloidin 568, Mitotracker Mitochondrial stain 641) in order to mark 8 cellular components (nucleus, endoplasmic reticulum, mitochondria, actin, Golgi, plasma membrane, nucleolus and RNA). Images at 20x magnification are then captured using a high content microscope Yokogawa Cell Voyager CV8000. These images go through a rigorous quality control process are then passed through the profiling pipeline using the open-source software Cell Profiler. Thousands of features are extracted from each image and value of each feature is computed so as to detect even the slightest phenotypic variation occurring in cells in an extremely sensitive manner.</p> <p>This dataset consists of profiles of 595 compounds from the EUbOPEN consortium (cell painting first batch) in 106 plates in the 384 well format. DMSO and positive controls are present in columns 1,2, 23 and 24. There are 39206 rows, each row corresponding to one well, and 7721 columns. The treatments have been done in a range of 8 doses and the highest dose treatment has been done at 2 time points. </p> <p> </p>
Data for: Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells
<p>Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly, despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.</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.