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1,411 results for “Cell States”
Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states
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Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration
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SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections
<p>The submitted dataset, correspond to the RAW (*.czi format) and analysis files of the 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>
Data from: Cell death and survival due to cytotoxic exposure modeled as a two-state Ising system
<p>Cancer chemotherapy agents are assessed for their therapeutic utility primarily by their ability to cause apoptosis of cancer cells and their potency is given by an IC50 value. Chemotherapy uses both target-specific and systemic-action drugs and drug combinations to treat cancer. It is important to judiciously choose a drug type, its dosage, and schedule for optimized drug selection and administration. Consequently, the precise mathematical formulation of cancer cells response to chemotherapy may assist in the selection process. In this paper, we propose a mathematical description of the cancer cell response to chemotherapeutic agent exposure based on a time-tested physical model of two-state multiple-component systems near criticality. We describe the Ising model methodology and apply it to a diverse panel of cytotoxic drugs administered against numerous cancer cell lines in a dose-response manner. The analyzed dataset was generated by the Netherlands Translational Research Center B.V.(Oncolines). This approach allows for an accurate and consistent analysis of cytotoxic agents' effects on cancer cell lines and reveals the presence or absence of the bystander effect through the interaction constant. By calculating the susceptibility function, we see the value of IC50 coinciding with the peak of this measure of the system's sensitivity to external perturbations.</p>
Development of equivalent circuit model for state of power estimation of NMC-based Li-ion cell
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Model Development for State-of-Power Estimation of Large-Capacity Nickel-Manganese-Cobalt Oxide-Based Lithium-Ion Cell Validated Using a Real-Life Profile
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Pollock: Fishing for Cell States
<p>Datasets, pretrained modules, and supplementary material for Pollock: Fishing for Cell States</p>
3D tissue cytometry analysis files for, "An atlas of healthy and injured cell states and niches in the human kidney"
<p>This deposit contains the supporting records of analysis for 3D cytometry presented in, "An atlas of healthy and injured cell states and niches in the human kidney". </p> <p>Contents:</p> <p>1) a collection of .zip files contains the 3D tissue cytometry files for tissue analyzed in the preprint doi: 10.1101/2021.07.28.454201. This collection includes the individual tissue specimens, XX-XXXX.zip, further described in detail in "Supplementary Table 2. 3D imaging and spatial transcriptomic experiments." </p> <p>2) neighborhoods by specimen as indicated above and calculated by Volumetric Tissue Exploration and Analysis (VTEA) for a radius of 50 voxels(accounting for anisotropy of voxels) or ~25 um as described in the methods of the preprint, doi: 10.1101/2021.07.28.454201.</p> <p>3) R environment file (.RData as a .zip file) for regenerating analysis from code at: https://github.com/KPMP/Cell-State-Atlas-2022</p> <p>Contents of XX-XXXX.zip files:</p> <p>1) maximum projections as used in the manuscript (all archived at kpmp.org)<br> 2) .obx and a .tif file which includes the segmented objects and associated measurements for use by VTEA (https://vtea.wiki/)<br> 3) .csv file including all the segmented objects and associated measurements<br> 4) .csv file including the neighborhood analysis results also found in the combined .zip file<br> 5) folder of ImageJ/FIJI folder which includes the expert ROIs and the pixel-wise consensus of ROIs drawn by experts used in cell classification strategy outlined in the methods<br> 6) folder of VTEA gate files and images of gating .png files used to label objects and used in cell classification strategy outlined in the methods of doi: 10.1101/2021.07.28.454201</p> <p>Please address any concerns or questions to the authors listed in the deposit or manuscript, doi: 10.1101/2021.07.28.454201.</p> <p> </p> <p> </p>
Seurat objects for "Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state" (https://doi.org/10.1038/s41467-023-42762-w)
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Dataset: Phytoplankton Cell-States: multiparameter lifetime flow monitoring reveals cellular heterogeneity: additional repeats
<p>Additional datasets of repeated experiments for Dataset: Phytoplankton Cell-States: multiparameter lifetime flow monitoring reveals cellular heterogeneity</p>
Effect of the overexpression of the GGP1 gene on cell wall remodelling and redox state in the tomato fruit
<p> </p> <p>The deposited data were collected as a part of the studies entitled ‘Effect of the overexpression of the GGP1 gene on cell wall remodelling and redox state in the tomato fruit’.</p> <p>The research is the result of cooperation between institutions: </p> <ul> <li>Group for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering (IMGGE) at the University of Belgrade (Serbia),</li> <li>Institute of Agrophysics, Polish Academy of Sciences (Poland),</li> <li>Department of Pharmaceutical Sciences, at the Aristotle University of Thessaloniki (Greece).</li> </ul> <p>The use of advanced microscopic techniques (immunolabeling method), methods of molecular biology (Western blotting), and biochemistry (HPLC, measurement of enzyme activities) allows for expanding knowledge in the field of plant cell physiology and horticulture. </p> <p> The attached files have been compressed to *.zip format. The dataset consists of the following files:</p> <p>A_1_Antioxidant enzymes activities</p> <p>A_2_CLSM imaging</p> <p>A_3_Native polyacrylamide electrophoresis of antioxidant enzymes</p> <p>A_4_Phenolic components in the fruit tissue</p> <p>A_5_Western Blotting with quantitative analysis</p>
Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy
<p>scRNA-seq read count matrices from patient-derived PDAC organoids.</p>
Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong></p> <p> </p> <p><strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup></p> <p> </p> <p><sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden</p> <p><sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan</p> <p><sup>* </sup>Contributed equally</p> <p><sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.</p>
Data associated with Cell Reports publication: Dura-Bernal et al. 2023, "Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics"
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data. The source code for the associated M1 model and data analysis can be found here: https://github.com/suny-downstate-medical-center/M1_NetPyNE_CellReports_2023</p> <p>Please download the data_v2.zip file, which contains the most updated and complete version of the data.</p> <p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Mixed model-based deconvolution of cell-state abundances along a one-dimensional trajectory [csd-eQTL]
<p><strong>README:</strong></p> <p>The full summary data of the cell-state-dependent eQTLs for GTEx Esophagus Mucosa (n=497) are stored in the .parquet format.</p> <p>An example of the file name:</p> <p><strong>"GTEx_Esophagus_Mucosa_bin1.cis_qtl_pairs.1.parquet.gz"</strong> means the summary data of csd-eQTLs for bin1 of chromosome 1.</p>
Case-Control Study of Renal Cell Cancer Among Caucasions and African Americans in the United States
ClinicalTrials.gov study NCT00340457. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Cultural Tailoring and Pilot Testing of an Inpatient Yoga Therapy Program for Cancer Patients Undergoing Hematopoietic Stem Cell Transplantation in India, Tanzania, and the United States
ClinicalTrials.gov study NCT05681026. IPD Sharing: Not stated. Countries: 3. Publications: 0.
Data from: Cell death and survival due to cytotoxic exposure modeled as a two-state Ising system
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Implementation of cell-free biological networks at steady state
<p>Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations. This reactor-based approach will allow testing of whether fundamental limits exist to in vitro network complexity.</p>
Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon
<p>Processed data use in the the Mellon manuscript</p> <p>The following scanpy anndata objects are also available</p> <ol> <li>preprocessed_t-cell-depleted-bm-rna.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data, cell-state densities, B-cell primed and lineage accessibility scores.</li> <li>preprocessed_t-cell-depleted-bm-atac.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, cell-state densities, B-cell primed and lineage peaks.</li> <li>preprocessed_t-cell-depleted-bm-rna-metacells.h5ad: Anndata object with metacells for the RNA modality of the T-cell depleted bone marrow multiome dataset .</li> <li>preprocessed_mouse-gastrulation-atlas.h5ad: Anndata object of the preprocessed mouse gastrulation data with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data,</li> </ol>
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.