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5,472 results for “mouse cells”
Single cell ATAC-seq Mouse Kidney Data: Chromatin-accessibility estimation from single-cell ATAC data with scOpen
<p>We provide results regarding the bioinformatic analysis of scATAC-seq from mouse UUO kidney at different time points.</p>
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration
<p>Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not inform the spatial context that is important for myogenic differentiation. Here, we demonstrate how large-scale integration of single-cell and spatial transcriptomic data can overcome these limitations. We created a single-cell transcriptomic dataset of mouse skeletal muscle by integration, consensus annotation, and analysis of 23 newly collected scRNAseq datasets and 88 publicly available single-cell (scRNAseq) and single-nucleus (snRNAseq) RNA-sequencing datasets. The resulting dataset includes more than 365,000 cells and spans a wide range of ages, injury, and repair conditions. Together, these data enabled identification of the predominant cell types in skeletal muscle, and resolved cell subtypes, including endothelial subtypes distinguished by vessel-type of origin, fibro/adipogenic progenitors defined by functional roles, and many distinct immune populations. The representation of different experimental conditions and the depth of transcriptome coverage enabled robust profiling of sparsely expressed genes. We built a densely sampled transcriptomic model of myogenesis, from stem cell quiescence to myofiber maturation and identified rare, transitional states of progenitor commitment and fusion that are poorly represented in individual datasets. We performed spatial RNA sequencing of mouse muscle at three time points after injury and used the integrated dataset as a reference to achieve a high-resolution, local deconvolution of cell subtypes. We also used the integrated dataset to explore ligand-receptor co-expression patterns and identify dynamic cell-cell interactions in muscle injury response. We provide a public web tool to enable interactive exploration and visualization of the data. Our work supports the utility of large-scale integration of single-cell transcriptomic data as a tool for biological discovery.</p>
Mass cytometry immunophenotyping data of two-week-old mouse pups' spleens depleted of maternal cells
<div> <div> <div> <p>The maternal cells transferred into the fetus during gestation persist long after birth in the progeny. These maternal cells have been hypothesized to promote the maturation of the fetal immune system in utero but there are still significant gaps in our knowledge of their potential roles after birth. To provide insights into these maternal cells' postnatal functional roles, we set up a transgenic mouse model to specifically eliminate maternal cells in the neonates by diphtheria toxin injection and confirmed significant depletion in the spleens. We then performed immunophenotyping of the spleens of two-week-old pups by mass cytometry to pinpoint the immune profile differences driven by the depletion of maternal cells in early postnatal life. We observed a heightened expression of markers related to activation and maturation in some natural killer and T cell populations. We hypothesize these results to indicate a potential postnatal regulation of lymphocytic responses by maternal cells. Together, our findings highlight an immunological influence of maternal microchimeric cells postnatally, possibly protecting against adverse hypersensitivity reactions of the neonate at a crucial time of new encounters with self and environmental antigens.</p> </div> </div> </div>
Single-cell RNA sequencing of mouse embryonic cells from the oocyte, 2-cell, 4-cell, 8-cell, blastocyst, and morula stages
<p>STRT-N is a newly optimized single-cell RNA sequencing method for studies of early genome activation in mammalian preimplantation development. Single embryos from the oocyte, 2-cell, 4-cell, 8-cell, blastocyst, and morula stages were sampled for experiments and were sequenced using STRT-N method. Here is the raw data from STRTN-seq. FASTQ files are available in <a href="https://www.ebi.ac.uk/biostudies/studies/S-BSST976">BioStudies database</a>.</p>
Microscopy-based assessment of RNA polymerase II clusters during differentiation of cultured mouse embryonic stem cells
<p>This repository contains the data and MatLab analysis scripts of the analysis of RNA polymerase II clusters over the course of differentiation of cultured mouse embryonic stem cells (mESCs). The cells were induced towards differentiation by either withdrawal of lineage-inhibiting factors (-LIF) or by RHB treatment. Both treatments were carried out in duplicate in independent experiments. Time course data were obtained by collection of cells at 3, 6, 12, 24, and 48 hours following the beginning of induction. Control data from unindexed cells were obtained at 24 and 48 hours. Cells were cultured, treated, collected, and fixed at University Medical Center Göttingen by Yomna Gohar, Priya Kumar, and Carmelo Ferrai. Fixed cells were fluorescently labeled and microscopy images were recorded and analyzed at Karlsruhe Institute of Technology by Lennart Hilbert. </p> <p>To analyse date data, the raw image data are first extracted into MatLab-native files using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/MultiPosition_extraction_nd2.m">MultiPosition_extraction_nd2.m</a> script. The actual analysis is then carried out using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ClusterAnalysis.m">ClusterAnalysis.m</a> script. Example microscopy images were produced using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ExampleImages.m">ExampleImages.m</a> script. The extracted data can be reviewed using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ReviewExtractedStacks.m">ReviewExtractedStacks.m</a> script.</p> <p>This is the main repository, containing the image analysis scripts alongside the links to the raw image data used in the analysis. The raw data are too large to be stored within this single repository, and therefore can be found at the following additional addresses.</p> <p>Differentiation by withdrawal of lineage-inhibiting factors (-LIF): <a href="https://doi.org/10.5281/zenodo.8013281">10.5281/zenodo.8013281</a></p> <p>Differentiation with addition of RHB for neuronal fate induction (RHB): <a href="https://doi.org/10.5281/zenodo.8013307">10.5281/zenodo.8013307</a></p>
PANDA cell-type-specific networks for S858R and WT mouse cerebral cortex
<p>The below files are from the data/results directory of this associated project and include the following:</p> <ul> <li><strong>PANDA networks </strong>: cell-type-specific TF-gene regulatory networks constructed using multi-omic inputs (snRNA-seq, TF-motif, and PPI) for all cell types in S858R and WT mouse cerebral cortex tissues (n = 16). All the files included for PANDA networks indicate the condition (heterozygous or control), tissue (cerebral cortex) followed by _PANDA.Rdata. (example: astrocytes_heterozygouscortexexpression_PANDA.Rdata)</li> </ul>
PANDA cell-type-specific networks for S858R and WT mouse kidney
<p>The below files are from the data/results directory of this associated project and include the following:</p> <ul> <li><strong>PANDA networks</strong> : cell-type-specific TF-gene regulatory networks constructed using multi-omic inputs (snRNA-seq, TF-motif, and PPI) for all cell types in S858R and WT kidney tissues (n = 34). All the files included for PANDA networks indicate the condition (heterozygous or control), tissue (kidney) followed by _PANDA.Rdata. (example: pericytes_heterozygouskidneyexpression_PANDA.Rdata)</li> </ul>
Single-cell and spatially resolved transcriptomic data of mouse regenerative livers under normal and fibrotic conditions
<p>A single-cell spatial-temporal transcriptomic atlas of liver regeneration under normal and fibrotic condition, including a total of 30 mouse liver samples obtained from 15 normal and 15 fibrotic mice at timepoints Day 0, 1, 2, 3, and 7 after a partial hepatectomy (PHx) procedure with three replicates for each time point, followed by the scRNA-seq and SRT sequencing for each sample using the Stereo-seq platform. </p>
Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
<p>These files contain the raw sequencing data (demultiplexed, unaligned BAM files or FASTQ files) collected as part of following manuscript: "Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types.". Included are oxidized and unoxidized small RNA sequencing libraries collected from RKO cells (human cell line, timecourse for methyltransferase expression), M. musculus B cells (splenic, CD43 depleted; methyltransferase under Cd79a-Cre driver), M. Musculus Plasma cells (sorted, methyltransferase under Bhlha15-Cre driver). </p><p> </p>
Mouse Cancer Cell-containing Macrobeads in the Treatment of Human Cancer
ClinicalTrials.gov study NCT00283075. IPD Sharing: NO. Countries: 1. Publications: 8.
Single-cell spatial transcriptomics of an inducible destabilized-domain Cre mouse line to target disease associated microglia
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Cone bipolar cell synapses generate transient versus sustained signals in parallel ON pathways of the mouse retina
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Intermittent ERK oscillations downstream of FGF in mouse embryonic stem cells
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Mass cytometry immunophenotyping data of two-week-old mouse pups' spleens depleted of maternal cells
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Data from: Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug
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Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data
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Compromised 2-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers
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Data from: Effect of stretching on inflammation in a subcutaneous carrageenan mouse model analyzed at single-cell resolution
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Data from: Mouse gingival single cell transcriptomic atlas identified a novel fibroblast subpopulation activated to guide oral barrier immunity in periodontitis
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Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states
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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.