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996 results for “mouse brain”
Enhanced and unified anatomical labeling for a common mouse brain atlas
<p>Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin and Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, here we adopt the FP labels into the CCF to merge two labels in the single atlas framework. We use cell type specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, detailed segmentations are added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we digitize our anatomical labels based on the Allen ontology, create a web-interface for visualization, and provide tools for comprehensive comparisons between the CCF and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.</p>
Data from: Multi-omics investigation reveals benzalkonium chloride disinfectants alter sterol and lipid homeostasis in the mouse neonatal brain
Lipids are critical for neurodevelopment; therefore, disruption of lipid homeostasis by environmental chemicals is expected to have detrimental effects on this process. Previously, we demonstrated that the benzalkonium chlorides (BACs), a class of commonly used disinfectants, alter cholesterol biosynthesis and lipid homeostasis in neuronal cell cultures in a manner dependent on their alkyl chain length. However, the ability of BACs to reach the neonatal brain and alter sterol and lipid homeostasis during neurodevelopment in vivo has not been characterized. Therefore, the goal of this study was to use targeted and untargeted mass spectrometry and transcriptomics to investigate the effect of BACs on sterol and lipid homeostasis, and to predict the mechanism of toxicity of BACs on neurodevelopmental processes. After maternal dietary exposure to 120 mg BAC/kg body weight/day, we quantified BAC levels in the mouse neonatal brain, demonstrating for the first time that BACs can cross the blood-placental barrier and enter the developing brain. Transcriptomic analysis of neonatal brains using RNA sequencing revealed alterations in canonical pathways related to cholesterol biosynthesis, liver X receptor-retinoid X receptor (LXR/RXR) signaling, and glutamate receptor signaling. Mass spectrometry analysis revealed decreases in total sterol levels and downregulation of triglycerides and diglycerides, which were consistent with the upregulation of genes involved in sterol biosynthesis and uptake as well as inhibition of LXR signaling. In conclusion, these findings demonstrate that BACs target sterol and lipid homeostasis and provide new insights for the possible mechanisms of action of BACs as developmental neurotoxicants.
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>
Mouse brain slices part 2
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Dataset related to article: "Fluoxetine increases brain MeCP2 immuno-positive cells in a female Mecp2 heterozygous mouse model of Rett syndrome through endogenous serotonin. "
<pre>Dataset related to article: "Fluoxetine increases brain MeCP2 immuno-positive cells in a female Mecp2 heterozygous mouse model of Rett syndrome through endogenous serotonin." </pre>
Mouse Brain Sagittal View - White
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A longitudinal MRI dataset of young adult C57BL6J mouse brain
<p>This dataset contains 101 labeled young adult C57BL6J mouse brain MRI scans acquired with a 11.7T MR scanner. As part of the source domain data of Brain Extraction Net (BEN), specific analysis and usage are provided at <a href="https://github.com/yu02019/BEN">github</a> and in the <a href="https://www.biorxiv.org/content/10.1101/2022.05.25.492956v2.abstract">manuscript</a>.</p> <p>Since T2WI is the most commonly used modality for rodent brain imaging and we have accumulated extensive brain scans with high-quality annotations in our previous research studies, we first trained the model on the Mouse-T2WI-11.7T dataset, which served as the source-domain dataset, following the conventional fully supervised training strategy.</p> <p>In particular, we focus on the following features:</p> <ul> <li><strong>Transferability and flexibility</strong>: BEN can adapt to different species, modalities and platforms through its adaptive batch normalization module and semi-supervised learning module.</li> <li><strong>Automatic quality assessment</strong>: Unlike traditional toolboxes, which rely on manual inspection to assess the brain extraction quality, BEN incorporates a quality assessment module to automatically evaluate its brain extraction performance.</li> <li><strong>Speed</strong>: As a DL-based method, BEN can process an MRI volume faster (<1 second) than traditional toolboxes (several minutes or longer).</li> </ul> <p> </p>
3D ground truth annotations of cleared whole mouse brain nuclei imaged with a mesoSPIM system
<p>Please see Achard et al. 2024 for Data Card and other information.</p>
Mouse with RNN brain
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A Multi-Scale Neuron Morphometry Dataset from Peta-voxel Mouse Whole-Brain Images
<p><span>Neuron morphology and sub-neuronal patterns offer vital insights into cell typing and the structural organization of brain networks. The community-collaborative BRAIN Initiative Cell Census Network (BICCN) project has yielded a vast amount of whole-brain imaging data. However, reconstructing multi-scale neuron morphometry at a whole-brain scale requires not only the integration of diverse hardware devices, tools, and algorithms but also a dedicated production workflow. To address these challenges, we developed a cloud-based, collaborative platform capable of handling peta-scale imaging data. Using this platform, we generated the largest multi-scale morphometry dataset from hundreds of sparsely labeled mouse brains. The morphometry dataset comprises 182,497 annotated cell bodies, 15,441 locally traced morphologies, and 1,876 fully reconstructed morphologies. We also identified sub-neuronal arborizations for both axons and dendrites, along with the primary axonal tracts connecting them. In addition, we identified 2.63 million putative boutons. All morphometric data were registered to the Allen Common Coordinate Framework (CCF) atlas. The morphometry dataset has proven to be an invaluable resource for whole-brain cross-scale morphological studies in mouse.</span></p>
mouse brain slices 1
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Ixiaro as Booster After Mouse-brain Derived Vaccines for Japanese Encephalitis
ClinicalTrials.gov study NCT01386827. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Safety and Efficacy Study of ChimeriVax™-JE and JE Inactivated Mouse Brain Vaccine in Children of Descending Age
ClinicalTrials.gov study NCT00441259. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Multi-omics investigation reveals benzalkonium chloride disinfectants alter sterol and lipid homeostasis in the mouse neonatal brain
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Data from: MRI mouse brain data of ischemic lesion after transient middle cerebral artery occlusion
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Data from: Correlations of behavioral deficits with brain pathology assessed through longitudinal MRI and histopathology in the HDHQ150/Q150 mouse model of Huntington's disease
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Data from: Influence of full-length dystrophin on brain volumes in mouse models of Duchenne muscular dystrophy
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Data from: Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain
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Enhanced and unified anatomical labeling for a common mouse brain atlas
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Gene responses in mouse brain to long-term exposure to microgravity
The spaceflight experiment was carried out using male C57BL/10J mice (8 weeks old at launch). Wild type mice (n=3) were launched by Space Shuttle Discovery and housed on the International Space Station (ISS) for 91 days. They returned to the Earth by Space Shuttle Atlantis. But only one mouse returned to the Earth alive. Whole brain was sampled from the mouse killed by inhalation of carbon dioxide at the Life Sciences Support Facility of Kennedy Space Center within 3-4 hours after landing. After the spaceflight experiment the on-ground experiment was also carried out at the Advanced Biotechnology Center in Genova Italy. A mouse with the same species sex and age was housed in mice drawer system (MDS) which was utilized for the spaceflight (SF) mice for 3 months as the ground control (GC). Another mouse was housed in normal vivarium cage as the laboratory control (LC). Amount of food and water supplementation and environmental conditions were simulated as the flight group. After 3 months brain was sampled from one mouse in group GC and LC respectively. Comprehensive analyses of gene expression were performed in the right brain. Total of 4,000 genes were analyzed. The expression levels of 60 genes significantly changed in response to SF compared with LC and/or GC. The 15 and 16 genes were up- (> 2 folds) and down-regulated (< 0.5 folds) respectively following SF vs. GC. The levels of 58 genes were significantly altered by housing in MDS in space and/or on the ground. Forty seven and 11 genes were significantly up- and down-regulated vs. LC. Twenty seven out of these genes responded to caging in MDS both in space and on the ground. Further 31 genes were influenced by housing in MDS on the Earth. Responses of the characteristics of brain to long-term gravitational unloading were investigated in mice.
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.