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5,472 results for “mouse cells”
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run4-1)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 4-1; the files are splited two two parts because of limitations of file size).</p>
Deep Learning Based Models for Preimplantation Mouse and Human Embryos Based on Single Cell RNA Sequencing
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Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2
<p>The chromatin accessibility assay using scNanoATAC-seq2 was conducted on the Oxford Nanopore (ONT) long-read sequencing platform and focused on samples related to mouse preimplantation development. These samples included preimplantation embryos, ranging from the zygote to the late blastocyst, as well as oocytes, granulosa cells, and naive mouse embryonic stem cells. The embryos were derived from crosses of C57xDBA, DBAxC57, and C57xCAST. Additionally, cell lines from humans and mice were assayed during the technical testing phase.</p> <p> </p> <p><strong>Note: </strong>In this dataset, 'pre-TE' denotes early trophectoderm (early TE), while 'TE' signifies late trophectoderm (late TE), as outlined in the main article.</p>
All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells
<p>Previously we showed that the vitamin A metabolite all-trans retinoic acid (atRA) induces synaptic plasticity in acute brain slices prepared from the mouse and human neocortex (Lenz et al., 2021). Depending on the brain region studied, distinct effects of atRA on excitatory and inhibitory neurotransmission have been reported. Here, we used intraperitoneal injections of atRA (10 mg/kg) in adult C57BL/6J mice to study the effects of atRA on excitatory and inhibitory neurotransmission in the mouse fascia dentate – a brain region implicated in memory acquisition. <span><span>No major changes in synaptic transmission were observed in the ventral hippocampus while a significant increase in both sEPSC frequencies and synapse numbers were evident in the dorsal hippocampus 6 hours after atRA administration.</span></span> The intrinsic properties of hippocampal dentate granule cells were not significantly different and hippocampal transcriptome analysis revealed no essential neuronal changes upon atRA treatment. In light of these findings, we tested for the metaplastic effects of atRA, i.e., for its ability to modulate synaptic plasticity expression in the absence of major changes in baseline synaptic strength. Indeed, in vivo long-term potentiation (LTP) experiments demonstrated that systemic atRA treatment improves the ability of dentate granule cells to express LTP. The plasticity-promoting effects of atRA were not observed in synaptopodin-deficient mice, therefore, extending our previous results regarding the relevance of synaptopodin in atRA-mediated synaptic strengthening in the mouse prefrontal cortex. Taken together, our data show that atRA mediates synaptopodin-dependent metaplasticity in mouse dentate granule cells.</p>
Mouse Kidney Atlas (MKA) & MKA-Extended: Single-cell and single-nucleus reference atlases of the mouse kidney
<p>This deposit contains two linked datasets of the mouse kidney:<br><br></p> <h4><strong>1. MKA (Mouse Kidney Atlas)</strong></h4> <p>A comprehensive reference atlas of the healthy adult mouse kidney, generated by integrating approximately <strong>140,000 cells and nuclei</strong> from <strong>59 publicly available single-cell and single-nucleus RNA-sequencing datasets</strong> across <strong>eight independent studies</strong>.<br>The MKA harmonizes annotations through a <strong>hierarchical cell-type model</strong>, enabling robust cross-study comparisons and accurate labeling of novel or rare cell populations.</p> <ul> <li> <p><strong>Original publication:</strong> Novella-Rausell <em>et al.</em>, <em>iScience</em> (2023). <em>“A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery.” </em>DOI: <a target="_new" rel="noopener">10.1016/j.isci.2023.106877</a></p> </li> <li> <p><strong>Format:</strong> <code>AnnData</code> object (~141,401 observations × 3,000 genes)</p> </li> </ul> <h4><strong>2. MKA-Extended</strong></h4> <p>An expanded version of the MKA. This extended atlas incorporates <strong>immune, injury-induced, and polycystic kidney disease–specific</strong> cellular populations, providing a unified reference for <strong>Tangram-based deconvolution</strong> of spatial transcriptomics datasets.</p> <ul> <li><strong>Original publication: </strong>Yasinoglu <em>et al.</em>, <em>JASN</em>, (2025). <em>“Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease.” </em>DOI: 10.1681/ASN.0000000894</li> <li> <p><strong>Format:</strong> <code>AnnData</code> object (~303,791 observations × 12,156 genes)</p> </li> </ul>
Processed Single-cell RNA-seq Data for Exercise Rejuvenation Intervention on Mouse Subventricular Zone
<p>Exercise single-cell RNA-seq data of mouse subventricular zone (in processed Seurat object) used in the publication "Cell type-specific aging clocks to quantify aging and rejuvenation in regenerative regions of the brain" (preprint available at <a href="https://doi.org/10.1101/2022.01.10.475747">https://doi.org/10.1101/2022.01.10.475747</a>).</p>
Signalling pathway crosstalk stimulated by L-proline drives mouse embryonic stem cells
<p>Contains data and R code to reproduce paper models, statistics and plots</p>
All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells
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Data from: An experimental analysis of the molecular effects of trastuzumab (herceptin) and fulvestrant (falsodex), as single agents or in combination, on human HR+/HER2+ breast cancer cell lines and mouse tumor xenografts
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Data from: Early mechanistic events induced by low molecular weight polycyclic aromatic hydrocarbons in mouse lung epithelial cells: a role for eicosanoid signaling
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Data from: Nanotransfection-based vasculogenic cell reprogramming drives functional recovery in a mouse model of ischemic stroke
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Type-specific dendritic integration in mouse retinal ganglion cells
<p>Dataset for <a href="https://www.biorxiv.org/content/10.1101/753335v1.abstract">Ran et al (2020)</a>. These data can be read by Python (>3.6) and Pandas (>1.0.0):</p> <pre><code class="language-python">import pickle data = pickle.load(open('./data_raw.pickle', 'rb')) </code></pre> <p>Or use our custom scripts. For more details, see <a href="https://github.com/berenslab/rgc_dendrites">https://github.com/berenslab/rgc_dendrites</a>. </p>
Mesenchymal stem cell-derived extracellular vesicles reduce senescence and extend healthspan in mouse models of aging.
<p>Source data file</p>
Data from: An increase in immature β-cells lacking Glut2 precedes the expansion of β-cell mass in the pregnant mouse
A compensatory increase in β-cell mass occurs during pregnancy to counter the associated insulin resistance, and a failure in adaptation is thought to contribute to gestational diabetes. Insulin-expressing but glucose-transporter-2-low (Ins+Glut2LO) progenitor cells are present in mouse and human pancreas, being predominantly located in extra-islet β-cell clusters, and contribute to the regeneration of the endocrine pancreas following induced ablation. We therefore sought to investigate the contribution of Ins+Glut2LO cells to β-cell mass expansion during pregnancy. Female C57Bl/6 mice were time mated and pancreata were collected at gestational days (GD) 6, 9, 12, 15, and 18, and postpartum D7 (n = 4/time-point) and compared to control (non-pregnant) animals. Beta cell mass, location, proliferation (Ki67+), and proportion of Ins+Glut2LO cells were measured using immunohistochemistry and bright field or confocal microscopy. Beta cell mass tripled by GD18 and β-cell proliferation peaked at GD12 in islets (≥6 β-cells) and small β-cell clusters (1–5 β-cells). The proportion and fraction of Ins+Glut2LO cells undergoing proliferation increased significantly at GD9 in both islets and clusters, preceding the increase in β-cell mass and proliferation, and their proliferation within clusters persisted until GD15. The overall number of clusters increased significantly at GD9. Quantitative PCR showed a significant increase in Pdx1 presence at GD9 vs. GD18 or control pancreas, and Pdx1 was visualized by immunohistochemistry within both Ins+Glut2LO and Ins+Glut2HI cells within clusters. These results indicate that Ins+Glut2LO cells are likely to contribute to β-cell mass expansion during pregnancy.
Data from: The functional diversity of retinal ganglion cells in the mouse
In the vertebrate visual system, all output of the retina is carried by retinal ganglion cells. Each type encodes distinct visual features in parallel for transmission to the brain. How many such 'output channels' exist and what each encodes are areas of intense debate. In the mouse, anatomical estimates range from 15 to 20 channels, and only a handful are functionally understood. By combining two-photon calcium imaging to obtain dense retinal recordings and unsupervised clustering of the resulting sample of more than 11,000 cells, here we show that the mouse retina harbours substantially more than 30 functional output channels. These include all known and several new ganglion cell types, as verified by genetic and anatomical criteria. Therefore, information channels from the mouse eye to the mouse brain are considerably more diverse than shown thus far by anatomical studies, suggesting an encoding strategy resembling that used in state-of-the-art artificial vision systems.
Single cell RNA-seq transcriptomic profile of circulating immune and progenitor cells in a mouse model of neonatal hypoxic/ischemic (HI) brain damage.
<p>Hematopoietic cells play a pivotal role in regulating the inflammatory and reparative immune responses triggered after ischemic tissue damage. The response initiated within the injured tissue leads to compositional and transcriptional changes in circulating hematopoietic and progenitor cells, which have been utilized as biomarkers. While the importance of different immune and progenitor cell subtypes in the development of ischemic damage has been extensively researched in adult tissue injuries, there has been limited investigation in neonates. This is a critical developmental stage where ischemic damage can result in severe and irreversible health consequences if not promptly treated. To determine how ischemic damage could affect circulating cells in neonates, we have induced hypoxic-ischemic (HI) brain damage in seven-day-old mice, characterized by focal white and gray-matter injury (Rice-Vannucci model). Brain damage and circulating cells were analyzed at 48h post-HI, the intermediate reparative/inflammatory response phase post-injury. We applied scRNAseq to dissect the transcriptional and cellular composition changes in the peripheral blood of HI-treated and SHAM control neonates. This study provides the first scRNAseq dataset for immune and progenitor circulating cells in newborns with cerebral HI damage. It may help to identify biomarkers and selective therapeutic approaches aimed at modulating inflammatory and reparative pathways. </p><p>CD1 postnatal day 7 (P7) mice were subjected to hypoxic/ischemic (HI) brain injury by permanent ligation of the left common carotid artery followed, after 2h recover, by relocation to a hypoxia chamber for 90 minutes. Sham control mice (SHAM) underwent a skin incision and wound closure followed by hypoxia exposure. Circulating blood cells were collected from SHAM and HI mice at P9. After red blood cells (RBC) lysis, 7AAD-Ter119- cells were FACS sorted and analysed using sc RNAseq. Other samples were FACS sorted for CD45+CD11+ and CD45-CD31+ cells and mixed.</p>
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and function types
<p>The hypothalamic paraventricular nucleus (PVN) is a highly complex brain region that is crucial for homeostatic<br> regulation through neuroendocrine signalling, outflow of the autonomic nervous system (ANS), and projections<br> to other brain areas. The past years, single-cell datasets of the hypothalamus have contributed immensely<br> to the current understanding of the diverse hypothalamic cellular composition. While the PVN has been<br> adequately classified functionally, its molecular classification is currently still insufficient.</p> <p>To address this, we created a detailed atlas of PVN transcriptional cell types by integrating various PVN<br> single-cell datasets into a recently published hypothalamus single-cell transcriptome atlas. Furthermore, we<br> functionally profiled transcriptional cell types, based on relevant literature, existing retrograde tracing data<br> and existing single-cell data of a PVN-projection target region.</p>
Figure 2 from: Hartati FK, Nafisah W, Sutanto A, Saati EA, Khairoh M, Sjamsiah (2024) Aqueous black rice (Oryza sativa L. indica) extract enhanced the activation of CD4+ and CD8+ T cells in mouse breast cancer model. Pharmacia 71: 1-7. https://doi.org/10.3897/pharmacia.71.e113442
Figure 2 Aqueous black rice (ABR) extract reduced the relative number of CD4+IL17+, CD4+TNFα+, and CD4+IFNγ+ cytokine production. A, C, E. were flow cytometry diagram; B, D, F. were the graph of flow cytometry results. The bar in the graph shows the calculation results as the mean ± SD of the relative number of cytokine production. *P<0.05, indicate significant different. The group in this study were normal group; Cancer, DMBA 15 mg/kg BW; Cis, DMBA 15 mg/kg BW + Cisplatin 5 mg/kg BW; ABR1, DMBA 15 mg/kg BW + aqueous black rice extract 0.2 g/kg BW; ABR2, DMBA 15 mg/kg BW + aqueous black rice extract 0.3 g/kg BW; ABR3, DMBA 15 mg/kg BW + aqueous black rice extract 0.4 g/kg BW; ABR4, DMBA 15 mg/kg BW + aqueous black rice extract 0.5 g/kg BW.
Figure 1 from: Hartati FK, Nafisah W, Sutanto A, Saati EA, Khairoh M, Sjamsiah (2024) Aqueous black rice (Oryza sativa L. indica) extract enhanced the activation of CD4+ and CD8+ T cells in mouse breast cancer model. Pharmacia 71: 1-7. https://doi.org/10.3897/pharmacia.71.e113442
Figure 1 Aqueous black rice (ABR) extract increased the relative number of CD4+CD62L- cells and CD8+CD62L- cells. A, C. Show flow cytometry diagrams, and B, D. Show graphs of the flow cytometry results. The bars in the graphs show the calculated results as the mean ± SD of the relative number of CD4+ and CD8+ cell activations. *P<0.05 indicates a significant difference. The groups in this study included the following groups: Normal; Cancer, DMBA 15 mg/kg BW; Cis, DMBA 15 mg/kg BW + Cisplatin 5 mg/kg BW; ABR1, DMBA 15 mg/kg BW + ABR extract 0.2 g/kg BW; ABR2, DMBA 15 mg/kg BW + ABR extract 0.3 g/kg BW; ABR3, DMBA 15 mg/kg BW + ABR extract 0.4 g/kg BW; and ABR4, DMBA 15 mg/kg BW + ABR extract 0.5 g/kg BW.
Figure 3 from: Hartati FK, Nafisah W, Sutanto A, Saati EA, Khairoh M, Sjamsiah (2024) Aqueous black rice (Oryza sativa L. indica) extract enhanced the activation of CD4+ and CD8+ T cells in mouse breast cancer model. Pharmacia 71: 1-7. https://doi.org/10.3897/pharmacia.71.e113442
Figure 3 Aqueous black rice (ABR) extract effect on mammary mice histology based on Hematoxylin & Eosin staining (M: 400x). D, ductal; AT, adipose tissue; arrow, cancer cell. The group in this study were normal group; Cancer, DMBA 15 mg/kg BW; Cis, DMBA 15 mg/kg BW + Cisplatin 5 mg/kg BW; ABR1, DMBA 15 mg/kg BW + aqueous black rice extract 0.2 g/kg BW; ABR2, DMBA 15 mg/kg BW + aqueous black rice extract 0.3 g/kg BW; ABR3, DMBA 15 mg/kg BW + aqueous black rice extract 0.4 g/kg BW; ABR4, DMBA 15 mg/kg BW + aqueous black rice extract 0.5 g/kg BW.
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.