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2,709 results for “Mouse Model”
Multiscale Entropy Analysis of Retinal Signals Reveals Reduced Complexity in a Mouse Model of Alzheimer's Disease
<p>MEA recordings from wild-type and 5xFAD mice retinas used for the analyses in the manuscript "Multiscale Entropy Analysis of Retinal Signals Reveals Reduced Complexity in a Mouse Model of Alzheimer's Disease".</p>
Article: Modeling Mouse ICM - Partial Data Bank
<p>Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.</p>
Boosting serotonin synthesis is not sufficient to improve motor coordination of Mecp2 heterozygous mouse model of Rett syndrome
<p>Excel file related to the article</p>
Deep Learning Based Models for Preimplantation Mouse and Human Embryos Based on Single Cell RNA Sequencing
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Data: Limiting hearing loss in transgenic mouse models
<p>A collection of post-processing data chunks used for generating figures for the publication <em>Limiting hearing loss in transgenic mouse models. </em>Each folder corresponds to an individual mouse involved in the study and includes datum generated from widefield and two-photon imaging (ROIs, flourescence values, etc.).</p>
Article: Modeling Mouse ICM - Complete Data Bank - Part II
<p>Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.</p>
Article: Modeling Mouse ICM - Complete Data Bank - Part III
<p>Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.</p>
Article: Modeling Mouse ICM - Complete Data Bank - Part I
<p>Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.</p>
Data from: A mouse model of cochlear implantation with chronic electric stimulation
Objectives: Cochlear implants provide an effective treatment option for those with severe hearing loss, including those with preserved low frequency hearing. However, certain issues can reduce implant efficacy including intracochlear tissue response and delayed loss of residual acoustic hearing. We describe a mouse model of cochlear implantation with chronic electric stimulation that can be used to study cochlear implant biology and related pathologies. Methods: Twelve normal hearing adult CBA/J mice underwent unilateral cochlear implantation and were evenly divided into one group receiving electric stimulation and one not. Serial impedance and neural response telemetry (NRT) measurements were made to assess implant functionality. Functionality was defined as having at least one electrode with an impedance 35 kOhms. Mouse cochleae were harvested for histology and 3D X-ray microscopy 21 days post-operatively, or, in case the implant was still functional, at a later time point when the implant failed. A separate experiment measured the hearing preservation rate in 7 adult CBA/J mice undergoing unilateral cochlear implantation with serial auditory brainstem response (ABR) and distortion product otoacoustic emissions (DPOAE). Results: Implants maintained functionality for a mean of 35 days in the non-stimulated group and 19.8 days in the stimulated group. Reliable NRT and behavioral responses to electric stimulation were recorded. A robust intracochlear peri-implant tissue response with neo-ossification was seen in all cochleae. Six of seven mice maintained intact low frequency hearing up to 6 weeks following cochlear implantation. Conclusions: We demonstrate the feasibility of cochlear implantation and behaviorally significant electric stimulation in the mouse, with the potential for hearing preservation. This model may be combined with established mouse models of hearing loss and the large genetic and molecular research toolkit unique to the mouse for mechanistic and therapeutic investigations of cochlear implant biology.
Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function - data bundle
<p>This bundle is an archive of data files, configuration files, and scripts related to the manuscript "Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function".</p> <p> </p>
Processed data used for spatial analysis of DMD mouse models
<p>This repository contains seurat objects and .H5AD files that were used in the analysis described in the paper titled <strong>"Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models"</strong> Authors: L.G.M. Heezen, T. Abdelaal, M. van Putten, A. Aartsma-Rus, A. Mahfouz and P. Spitali</p> <p>It contains datafiles obtained from spatial transcriptomics (Visium, 10x Genomics) experiments on skeletal muscle samples from two wildtypes: C57BL10 and DBA/2J and two DMD mouse models: mdx and D2-mdx. All ten weeks old male mice, 10micron thick sections of the quadriceps.</p>
Dataset for "DSCAM gene triplication causes excessive GABAergic synapses in the neocortex in Down syndrome mouse models"
<p>Dataset for manuscript entitled "DSCAM gene triplication causes excessive GABAergic synapses in the neocortex in Down syndrome mouse models"</p>
rMATS analysis of alternative splicing events in a mouse model of environmental liver disease
<p>rMATS (https://rnaseq-mats.sourceforge.io/) was used to identify differential alternative splicing events (ASEs) corresponding to all five major types of AS patterns, <em>i.e</em>., skipped exon (SE), mutually exclusive exons (MXE), alternative 3’ splice site (A3SS), alternative 5’ splice site (A5SS), and retained intron (RI), in the HFD-fed mouse livers exposed to Ar1260, PCB126, or Ar1260 + PCB126 co-exposure compared to vehicle control This dataset identifies differential ASEs corresponding to all five major types of AS patterns [<em>i.e.,</em> skipped exon (SE), mutually exclusive exons (MXE), alternative 3’ splice site (A3’SS), alternative 5’ splice site (A5’SS), and retained intron (RI)], between Ar1260, PCB126, and Ar1260 + PCB126-exposed samples and vehicle control. For each ASE, the estimation of the alternatively spliced region usage is defined as percent-spliced in (ψ or PSI). Each comparison was made to identify differential ASEs with an associated change in exon usage (∆ψ). Differential ASEs were detected with an FDR of <0.05 and |∆ψ| of≥5%. The difference in the proportion of the two isoforms of the transcript was expressed as the change in mean percentage spliced-inform included (mean ∆ψ).</p>
Dataset related to: Liver factor B silencing to cure C3 glomerulopathy: Evidence from a mouse model of complement dysregulation
<p>The files contain all the dataset included in the manuscript divided by figures.</p> <p>Abstract: Uncontrolled activation of the alternative pathway (AP) of complement, due to genetic and/or acquired defects, plays a primary pathogenetic role in C3 glomerulopathy (C3G), a rare and heterogeneous disease characterised by predominant C3 fragment deposition within the glomerulus, as well as glomerular damage. There are currently no approved disease-specific treatments for C3G, but new drugs that directly counteract AP dysregulation, targeting components of the pathway, have opened promising new perspectives for managing the disease. Complement factor B (FB), which is primarily synthesised by hepatocytes, is a key component of the AP, as it drives the central amplification loop of the complement system. In this study we used a GalNAc (N-Acetylgalactosamine)-conjugated siRNA to selectively target and suppress liver FB expression in two mouse models characterised by the complete (Cfh<sup>-/-</sup> mice) or partial (Cfh<sup>+/-</sup>) loss of function of complement factor H (FH). Homozygous deletion of FH induced a severe C3G phenotype, with strong dysregulation of the AP of complement, glomerular C3 deposition and almost complete C3 consumption. Mice with a heterozygous deletion of FH had intermediate C3 levels and exhibited slower disease progression, resembling human C3G more closely. Here we showed that FB siRNA treatment did not improve serum C3 levels, nor limit glomerular C3 deposition in Cfh<sup>-/-</sup> mice, while it did normalise circulating C3 levels, reduce glomerular C3 deposits, and limit mesangial electron-dense deposits in Cfh<sup>+/-</sup> mice. The present data provide important insights into the potential benefits and limitations of FB-targeted inhibition strategies and suggest RNA interference-mediated FB silencing in the liver as a possible therapeutic approach for treating C3G patients with FH haploinsufficiency.</p>
Ineffectual immunity in a resurrected mouse model of persistent viremia
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Data from: Near-infrared dual bioluminescence imaging in mouse models of cancer using infraluciferin
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Data from: Three-dimensional self-gated cardiac MR imaging for the evaluation of myocardial infarction in mouse model on a 3T clinical MR system
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Data from: Development of an adrenocortical cancer humanized mouse model to characterize anti-PD1 effects on tumor microenvironment
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Decreased content of ascorbic acid (vitamin C) in the brain of knockout mouse models of Na+, K+- ATPase-related neurologic disorders
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Data from: A mouse model of cochlear implantation with chronic electric stimulation
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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.