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11,105
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11,105 results for “single cells”
A Pan-Cancer Single-Cell RNA-seq Atlas of Intratumoral B Cells
<p>Seurat object associated with publication 'A Pan-Cancer Single-Cell RNA-seq Atlas of Intratumoral B Cells' (Fitzsimons et al. Cancer Cell 2024)</p>
Probabilistic Alignment of Single-Cell Data
Open the record for dataset details and reuse information.
Jind-Multi: An extended framework to leverage multiple labeled datasets for the automatic annotation of single-cell RNA and ATAC data
Open the record for dataset details and reuse information.
Data from: Specific membrane capacitance, cytoplasm conductivity and instantaneous Young's modulus of single tumour cells
As label-free biomarkers, biophysical properties of cells are widely used for cell type classification. However, intrinsic biophysical markers, e.g. specific membrane capacitance (Cspecific membrane), cytoplasm conductivity (σconductivity) and instantaneous Young's modulus (Einstantaneous) measured for hundreds of single cells were not yet reported. In this study, single cells in suspension (adherent cells treated with trypsin) were aspirated through a microfluidic constriction channel at 25°C, and the entry processes and impedance profiles were recorded and translated to Cspecific membrane, σconductivity and Einstantaneous. Cspecific membrane, σconductivity and Einstantaneous of five cell types were quantified as 2.10±0.38 μF/cm2, 0.91±0.15 S/m and 5.52±0.95 kPa for H460 cells (ncell=437); 2.52±0.54 μF/cm2, 0.83±0.12 S/m and 5.54±1.04 kPa for H446 cells (ncell=410); 2.45±0.57 μF/cm2, 0.99±0.18 S/m and 5.16±1.68 kPa for A549 cells (ncell=442); 1.86±0.31 μF/cm2, 1.07±0.18 S/m and 3.86±0.81 kPa for 95D cells (ncell=415); 2.03±0.35 μF/cm2, 0.99±0.16 S/m and 3.49±0.70 kPa for 95C cells (ncell=290). The database of Cspecific membrane, σconductivity and Einstantaneous may serve as a reference for future studies of cellular biophysical properties.
Data from: Stem cell differentiation trajectories in Hydra resolved at single-cell resolution
The adult Hydra polyp continually renews all of its cells using three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. We sequenced 24,985 Hydra single-cell transcriptomes and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified gene modules and putative regulators expressed along these trajectories, thus creating a comprehensive molecular map of all developmental lineages in the adult animal. In addition, we built a gene expression map of the Hydra nervous system. Our work constitutes a resource for addressing questions regarding the evolution of metazoan developmental processes and nervous system function.
Mechanical heterogeneity along single cell-cell junctions is driven by lateral clustering of cadherins during vertebrate axis elongation
<p>Morphogenesis is governed by the interplay of molecular signals and mechanical forces across multiple length scales. The last decade has seen tremendous advances in our understanding of the dynamics of protein localization and turnover at sub-cellular length scales, and at the other end of the spectrum, of mechanics at tissue-level length scales. Integrating the two remains a challenge, however, because we lack a detailed understanding of the subcellular patterns of mechanical properties of cells within tissues. Here, in the context of the elongating body axis of <i>Xenopus</i> embryos, we combine tools from cell biology and physics to demonstrate that individual cell-cell junctions display finely-patterned local mechanical heterogeneity along their length. We show that such local mechanical patterning is essential for the cell movements of convergent extension and is imparted by locally patterned clustering of a classical cadherin. Finally, the patterning of cadherins and thus local mechanics along cell-cell junctions are controlled by Planar Cell Polarity signaling, a key genetic module for CE that is mutated in diverse human birth defects.</p>
Longitudinal Single Cell Atlas Identifies Type I Interferon Response as an Early Transient Prognostic Signature of COVID-19 Severity
<p>The clinical spectrum of COVID-19 ranges from asymptomatic or mildly symptomatic illness to pneumonia, critical illness and death. Molecular markers early in the disease course (Days 1-8) that identify patients at high risk for progression are scarce, due to the paucity of relevant longitudinal studies. We performed longitudinal single cell RNA-seq on 286 peripheral blood samples from 108 age- and gender-matched COVID-19 patients, 73 of which had at least one early sample. By examining discrete cell subtypes as well as continuous single cell states, we identified upregulation of genes related to type I interferon (IFN) signaling as the predominant cellular prognostic signature of future disease severity. Type I IFN signaling was dynamic and complex, spiking early in Progressors and then receding to the level of Non-Progressors at the very next sampling. Across the entire cohort, expression of type I IFN signaling genes dropped steadily, falling to asymptomatic levels by Day 14 regardless of severity. Moreover, in severe and critical cases, IFN signaling was deficient during Days 5-8, potentially due to upregulation of <em>SOCS3</em> and other negative regulators. In summary, we have identified an early expression signature that may predict COVID-19 severity, as well as potential mechanisms underlying the dysfunctional host immune response in severe disease.</p>
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data
<p>This dataset contains gene expression values, i. e. transcript counts, of 278 intestinal epithelial cells.</p>
Inter and Intra-tumour Heterogeneity of Paediatric-type Diffuse High-Grade Glioma Revealed by Single-Cell Mass Cytometry
<p>raw data (fcs file) from mass cytometry experiments </p>
Enhancing single-cell proteomics through tailored Data-Independent Acquisition and micropillar array-based chromatography
<p>This repository contains all the tables exported from Spectronaut.</p>
demo data curras-alonso_murine_single_cell_atlas
<p>demo data for curras-alonso_murine_single_cell_atlas</p>
Text-fig. 23. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Longitudinal section (orthoslice yz0827) showing fruitlet with apical stigmatic region and a single seed enclosed within the fruitlet wall that has a thick epidermal cuticle; note the tiny embryo (emb) internal to the micropyle (mi) and oriented toward the base of the fruitlet; b) Transverse section through apical part of two fruitlets (orthoslice xy0810) showing the fruitlet wall (fr) composed of small thin-walled cells covered by an epidermis of isodiametric cells (ep) with a thick outer cuticle (cu); c) Longitudinal section (orthoslice xz0370) through basal part of fruitlet perpendicular to section in (a) showing the micropyle (mi), embryo (emb) composed of tiny cells, and the thick cuticle (cu) covering the bulging cells of the fruitlet epidermis. Specimen, Catefica 50-S174907 (a–c). Scale bars = 300 Μm (a–c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 23. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Longitudinal section (orthoslice yz0827) showing fruitlet with apical stigmatic region and a single seed enclosed within the fruitlet wall that has a thick epidermal cuticle; note the tiny embryo (emb) internal to the micropyle (mi) and oriented toward the base of the fruitlet; b) Transverse section through apical part of two fruitlets (orthoslice xy0810) showing the fruitlet wall (fr) composed of small thin-walled cells covered by an epidermis of isodiametric cells (ep) with a thick outer cuticle (cu); c) Longitudinal section (orthoslice xz0370) through basal part of fruitlet perpendicular to section in (a) showing the micropyle (mi), embryo (emb) composed of tiny cells, and the thick cuticle (cu) covering the bulging cells of the fruitlet epidermis. Specimen, Catefica 50-S174907 (a–c). Scale bars = 300 Μm (a–c).
Ex vivo tissue perturbations coupled to single cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis
<p>Processed count tables of scRNA-seq data generated for this study.</p>
Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease (Invitro ArchR Object)
<p>This repo contains invitro ArchR object</p>
Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease (Invivo ArchR Object)
<p>This repo contains invivo ArchR object</p>
Confronting false discoveries in single-cell differential expression
<p>A repository containing 18 benchmarking datasets for single-cell method development.</p>
Single-cell profiling of complex plant responses to pathogen infection
<p>Original images for figures and quantifications. </p>
Cellular and molecular heterogeneities and signatures, and pathological trajectories of fatal COVID-19 lungs defined by spatial single-cell transcriptome analysis
<p>Spatial in-situ data analysis.</p>
Data for "A benchmark of computational pipelines for single-cell histone modification data"
<p>The `time_features.txt` and `time_correct.txt` files contain the runtimes for the various embedding methods.</p> <p>The .csv files contain the computed scores (both supervised and unsupervised) for all the methods.</p>
Single cell spatial analysis and biomarker discovery in Hodgkin lymphoma
<p>Imaging Mass Cytometry Data of Hodgkin Lymphoma. Details in associated manuscript</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.