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295 results for “midbrain”
Rapid sensorimotor adaptation to auditory midbrain silencing in free-flying bats
<p>This dataset accompanies the manuscript entitled "Rapid sensorimotor adaptation to auditory midbrain silencing in free-flying bats".<br>The structures contain the preprocessed data for each bat (individual structures for vocal and flight trajectory, or an overall structure for behavior). <br>The original code that allows for the figure generation associated with this manuscript is included. <br>The data for the audiograms and ABRs is also provided in csv format.</p>
Data from: Dynamic changes in chloride homeostasis coordinate midbrain inhibitory network activity during reward learning
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Data for: Developmental origins of Parkinson’s disease risk: perinatal exposure to the organochlorine pesticide dieldrin leads to sex-specific DNA modifications in critical neurodevelopmental pathways in the mouse midbrain
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Data from: Vocal repertoire expansion in singing mice by co-opting a conserved midbrain circuit node
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Data from: Microprism-based two-photon imaging of the mouse inferior colliculus reveals novel organizational principles of the auditory midbrain
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Data from: Developmental Dieldrin exposure alters DNA methylation at genes related to dopaminergic neuron development and Parkinson's disease in mouse midbrain
Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson's disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and ventral mesencephalon, containing primarily substantia nigra, were microdissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing (RRBS). We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (FDRNr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to subsequent toxic stimuli and contribute to the development of late-life neurodegenerative disease, including PD.
Data for Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration
<p>Raw Data for publication titled Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration.</p>
Single-cell RNAseq of Day 49 midbrain organoids from healthy and alpha-synuclein triplication iPSC lines
<p>Unbiased single-cell RNAseq of Day 49 midbrain dopaminergic organoids (10x 3' v3) of the Patikas et al. publication.</p> <p> </p> <p>The mono-unt-celltypes.h5ad refers to the object shown at Fig 2A and contains 3 cell lines:</p> <ol> <li>KOLF2 ( Control cell line)</li> <li>SNCA-3x alpha Synuclein triplication Parkinson's Disease patient-derived iPSC line</li> <li>SNCA-corr (SNCA-3x isogenic control with the triplication mutation corrected)</li> </ol> <p>The all-celltypes.h5ad refers to the object shown at Fig 4 onwards and contains the 3 cell lines that are included in model-dataset.h5ad and 7 other single-cell RNAseq samples:</p> <ol> <li>SNCA-3x+KOLF2 (chimera organoid condition of SNCA-3x and KOLF2 of iPSCs grown together in a midbrain organoid)</li> <li>SNCA-corr+KOLF2 (chimera organoid condition of SNCA-corr and KOLF2 of iPSCs grown together in a midbrain organoid)</li> <li>5 paired rotenone conditions. For each condition (KOLF2, SNCA-3x, SNCA-corr, SNCA-3x+KOLF2, SNCA-corr+KOLF2) a paired condition with acute 24h rotenone treatment in an antioxidant-free medium.</li> </ol>
High-density electrode recordings reveal strong and specific connections between retinal ganglion cells and midbrain neurons.
<p>This is the source file to be use for debugging problems on your own set-up. This files is a good example to both the repository provided for visual processing on the Kremow GitHub:</p> <p>https://github.com/KremkowLab/Axon-on-Neuropixels-in-Kilosort</p> <p>https://github.com/KremkowLab/tangential_recording</p>
Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP
<p>This dataset corresponds to the research manuscript entitled "Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP"</p>
Data from: Midbrain encodes sound detection behavior without auditory cortex
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Developmental dieldrin exposure alters DNA methylation at genes related to dopaminergic neuron development and Parkinson’s disease in mouse midbrain
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Protein aggregation and calcium dysregulation are the earliest hallmarks of familial Parkinson's disease in human midbrain dopaminergic neurons
<p>Mutations in the <em>SNCA</em> gene cause autosomal dominant Parkinson’s disease (PD), with loss of dopaminergic neurons in the substantia nigra, and aggregation of α-synuclein. The sequence of molecular events that proceed from an <em>SNCA</em> mutation during development, to end stage pathology is unknown. Utilising human induced pluripotent stem cells (hiPSCs), we resolved the temporal sequence of SNCA induced pathophysiological events in order to discover early, and likely causative, events. Our small molecule-based protocol generates highly enriched midbrain dopaminergic (mDA) neurons: molecular identity was confirmed using single-cell RNA sequencing and proteomics, and functional identity through dopamine synthesis, and measures of electrophysiological activity. At the earliest stage of differentiation, prior to maturation to mDA neurons, we demonstrate the initial formation of small β-sheet rich oligomeric aggregates, in <em>SNCA</em>-mutant cultures. Aggregation persists and progresses, ultimately resulting in the accumulation of phosphorylated aggregates. Impaired intracellular calcium signalling, increased basal calcium, and impairments in mitochondrial calcium handling occurred early at day 34-41 post differentiation. Once midbrain identity fully developed, at day 48-62 post differentiation, <em>SNCA</em>-mutant neurons exhibited mitochondrial dysfunction, oxidative stress, lysosomal swelling and increased autophagy. Ultimately these multiple cellular stresses lead to abnormal excitability, altered neuronal activity, and cell death. Our differentiation paradigm generates an efficient model for studying disease mechanisms in PD, and highlights that protein misfolding to generate intraneuronal oligomers is one of the earliest critical events driving disease in human neurons, rather than a late-stage hallmark of the disease.</p>
BrainSTEM: A multi-resolution fetal brain atlas to assess the fidelity of human midbrain cultures
<p>This upload contains data objects associated with our paper "BrainSTEM: A multi-resolution fetal brain atlas to assess the fidelity of human midbrain cultures".</p> <p>In particular, this upload contains the in-house single-cell dataset (toh.inhouse) and 12 single-cell datasets from published literatures, totalling 13 query datasets, as R object files.</p> <p>Detailed information about the publicly available query datasets can be found in the Supplementary Table 6 of the paper abovementioned.</p> <p> </p> <p> </p>
CD3_CD68_PD_midbrain_counts
<p>This file contains quantification of interactions between CD3+ and CD68+ cells in the perivascular space of PD or neurological control midbrains.</p>
Human Embryonic Stem C ells-derived Immature Midbrain Dopaminergic Neurons Transplanted in Parkinsonian Mon-keys Recover Dopamine Levels and Motor Behavior
<p>Supplementary videos of the article "Human Embryonic Stem Cells-derived Immature Midbrain Dopaminergic Neurons Transplanted in Parkinsonian Mon-keys Recover Dopamine Levels and Motor Behavior"</p>
Midbrain dopaminergic inputs gate amygdala intercalated cell clusters by distinct and cooperative mechanisms in male mice
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Data from: Midbrain adaptation may set the stage for the perception of musical beat
The ability to spontaneously feel a beat in music is a phenomenon widely believed to be unique to humans. Though beat perception involves the coordinated engagement of sensory, motor, and cognitive processes in humans, the contribution of low-level auditory processing to the activation of these networks in a beat-specific manner is poorly understood. Here, we present evidence from a rodent model that midbrain pre-processing of sounds may already be shaping where the beat is ultimately felt. For the tested set of musical rhythms, on-beat sounds on average evoked higher firing rates than off-beat sounds, and this difference was a defining feature of the set of beat interpretations most commonly perceived by human listeners over others. Basic firing rate adaptation provided a sufficient explanation for these results. Our findings suggest that midbrain adaptation, by encoding the temporal context of sounds, creates points of neural emphasis that may influence the perceptual emergence of a beat.
Age-induced midbrain-striatum assembloid models early phenotypes of Parkinson's disease
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Tabular datasets for for Morrone Parfitt, G., Coccia, E., Goldman, C. et al. Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson's disease model. Nat Commun 15, 447 (2024). https://doi.org/10.1038/s41467-024-44732-2
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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.