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915 results for “wild mice”
SNP genotypes for 524 wild mice and selected laboratory strains
<p>SNP genotypes from the Mouse Universal Genotyping Array for 524 wild mice and 12 selected laboratory strains. Data are provided in PLINK binary format (*.bed/*.bim/*.fam files) with an accompanying sample manifest (comma-separated text.)</p>
RNA-seq based analysis of gene expression in thyroids of wild-type and Keap1 knockdown mice after exposure to excess iodide.
<p>C57BL/6J Keap1flox/flox mice were developed by Prof. Masayuki Yamamoto (DOI: 10.1016/j.bbrc.2005.10.185). These mice express lower levels of Keap1 because of the loxP site insertions (DOI: 10.1128/MCB.01591-09) and are designated as Keap1KD. 3-4 months old WT and Keap1KD mice fed a standard diet (KLIBA NAFAG 3242, Switzerland) containing 1.5 mg/kg sodium iodine were given normal tap water with or without 0.05% sodium iodide (Sigma, St Louis, MO, USA) for 7 days. Hence, the following groups of mice were included:</p> <p>WT mice on control water (n=8)-designated as wt in the file</p> <p>WT mice exposed to excess iodide (WT-IOD, n=6)- designated as wti in the file</p> <p>Keap1KD mice on control water (n=8)- designated as kp in the file</p> <p> and Keap1KD mice exposed to excess iodide (Keap1KD-IOD, n=6)- designated as kpI in the file. </p> <p> Mice were maintained in the animal facility of the Department of Physiology at the University of Lausanne in temperature-, light-, and humidity-controlled rooms with a 12-hour light/dark cycle. All animal procedures were in accordance with Swiss legislature and the study was approved by the Canton of Vaud SCAV.</p> <p>RNA from individual mouse thyroids was prepared as previously described (DOI: 10.1007/978-1-4939-3756-1_25) and was submitted to Alithea Genomics (Switzerland). The bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced as described previously (DOI: 10.1186/s13059-019-1671-x) to a depth of approximately 1.2 million raw reads per sample.</p> <p>This research was funded by the Swiss National Science Foundation Research Grants 310030_212558, IZCOZ0_205415 and IZCOZ0_177070</p> <p></p> <p></p>
Vocal communication is seasonal in social groups of wild, free-living house mice
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Data from: Sleep, inflammation, and cognitive behavior of aged wild-type mice subjected to diffuse brain injury and aged 3xTg-AD mice as a model of Alzheimer's disease
<p>Identifying differential responses between sexes following traumatic brain injury (TBI) can elucidate the mechanisms behind disease pathology. Peripheral and central inflammation in the pathophysiology of TBI can increase sleep in male rodents, but this remains untested in females. We hypothesized that diffuse TBI would increase inflammation and sleep in males more so than in females. Diffuse TBI was induced in C57BL/6J mice and serial blood samples were collected (baseline, 1, 5, 7 days post‐injury [DPI]) to quantify peripheral immune cell populations and sleep regulatory cytokines. Brains and spleens were harvested at 7DPI to quantify central and peripheral immune cells, respectively. Mixed‐effects regression models were used for data analysis. Female TBI mice had 77%–124% higher IL‐6 levels than male TBI mice at 1 and 5DPI, whereas IL‐1β and TNF‐α levels were similar between sexes at all timepoints. Despite baseline sex differences in blood‐measured Ly6Chigh monocytes (females had 40% more than males), TBI reduced monocytes by 67% in TBI mice at 1DPI. Male TBI mice had 31%–33% more blood‐measured and 31% more spleen‐measured Ly6G+ neutrophils than female TBI mice at 1 and 5DPI, and 7DPI, respectively. Compared with sham, TBI increased sleep in both sexes during the first light and dark cycles. Male TBI mice slept 11%–17% more than female TBI mice, depending on the cycle. Thus, sex and TBI interactions may alter the peripheral inflammation profile and sleep patterns, which might explain discrepancies in disease progression based on sex.</p>
Data from: Phenotypic resources immortalized in a panel of wild-derived strains of five species of house mice
<p>The house mouse, <em>Mus musculus</em>, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. To assess the proportion of variation added by wild progenitors, we estimated phenotypic variation in 84 WDS representing 5 species (<em>M. musculus</em>, <em>M. spretus</em>, <em>M. spicilegus</em>, <em>M. macedonicus</em>, <em>M. caroli</em>), 3 subspecies (<em>M. m. musculus</em>, <em>M. m. domesticus</em>, <em>M. m. castaneus</em>), and compared it with 5 CLS. The spectrum of WDS captures long-term mouse evolution, estimated to be over 5 million years ago since the split of <em>M. caroli</em> from the remaining mouse species. All mice are housed in a conventional breeding facility (without a nanofilter barrier or specific-pathogen free condition) at the Institute of Vertebrate Biology, Czech Academy of Sciences, in Studenec. They are maintained under standard conditions: light/dark regime of 14/10 hours, temperatures of 23 ± 1 °C during summer (April-September) and 22 ± 1 °C during winter (October-March), respectively, and relative humidity within 40-70 %. Mice have access to food pellets and tap water <em>ad libitum</em>. Further data on this mouse repository and WDS can be obtained at <a href="https://housemice.cz/en/strains/">https://housemice.cz/en/strains/</a>.</p> <p>Morphological traits were measured in 4335 mice and include body weight, spleen weight, body length, tail length, weight of both ovaries, sperm count, the weight of testes, left epididymis, and seminal vesicles. Reproductive ability was estimated in 87 WDS and 8 CLS. This dataset was obtained from 90,077 offspring born to 8,298 mothers in 17,049 litters recorded in Studenec studbooks between 2000 and 2023. Reproductive performance was characterized by litter size, newborn mortality (calculated as the proportion of stillborn or cannibalized mice across all litters), and the number of generations produced per year. We also estimated the time since a WDS was established from wild progenitors until completing 20 generations of strict brother-sister mating, i.e., the generation at which a strain of mice can be considered inbred.</p> <p>Although CLS resemble <em>M. m. domesticus</em> and<em> M. m. musculus </em>WDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The data suggest that WDS can be a useful tool in evolutionary studies, providing a basis for comparative analyses with other mammal taxa, particularly classical laboratory mice. The detected stunning phenotypic variation supplemented by genetic variation have great potential for medical applications.</p>
Single-Cell RNA-sequencing of neural precursor cells from an Alzheimer's mouse model, wild-type mice, and Alzheimer's mice rescued with Usp16 haploinsufficiency
<p class="MsoNormal">Alzheimer's disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify an earlier targetable phenotype. Utilizing a mouse model of AD we found that cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it one of the earlier defects in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. To delineate potential self-renewal pathways that might contribute to the defect and rescue of Tg-SwDI NPCs and Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup></em> NPCs, respectively, we performed single-cell RNA-seq and gene set enrichment analysis (GSEA) on lineage depleted primary FACS-sorted CD31<sup><span>-</span></sup>CD45<sup><span>-</span></sup>Ter119<sup><span>-</span></sup>CD24<sup><span>-</span></sup> NPCs from Tg-SwDI, WT, and Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup></em> mice at 3-4 months and 1 year of age. Using the GSEA Hallmark gene sets, we found only three gene sets that were enriched in Tg-SwDI mice over WT mice and rescued in the Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup> </em>mice at both ages: TGF-ß pathway, oxidative phosphorylation, and Myc Targets. The TGF-ß pathway consistently had the highest normalized enrichment score in pairwise comparisons between Tg-SwDI vs WT and Tg-SwDI vs Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup> </em>of the three rescued pathways. These data suggest that USP16 may regulate neural precursor cell function in part through the BMP pathway.</p>
Relationships between immune gene expression and circulating cytokine levels in wild house mice
<p>1. Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localisation of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital.</p> <p>2. Here we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus.</p> <p>3. Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e. the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood).</p> <p>4. Potential reasons for discrepancies between measures, including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions, and consider what might be inferred from immune assays.</p>
The genetics of immune and infection phenotypes in wild mice, Mus musculus domesticus
<p><span>Wild animals are under constant threat from a wide range of micro- and macroparasites in their environment. Animals make immune responses against parasites, and these are important in affecting the dynamics of parasite populations. Individual animals vary in their anti-parasite immune responses. Genetic polymorphism of immune-related loci contributes to inter-individual differences in immune responses, but most of what we know in this regard comes from studies of humans or laboratory animals; there are very few such studies of wild animals naturally infected with parasites. Here we have investigated the effect of Single Nucleotide Polymorphisms (SNPs) in immune-related loci (the MHC, and loci coding for cytokines and Toll-like receptors) on a wide range of immune and infection phenotypes in UK wild house mice, <em>Mus musculus domesticus</em>. We found strong associations between SNPs in various MHC and cytokine-coding loci on both immune measures (antibody concentration and cytokine production) and on infection phenotypes (infection with mites, worms and viruses). Our study provides a comprehensive view of how polymorphism of immune-related loci affects immune and infection phenotypes in naturally infected wild rodent populations.</span></p>
Data from: Single cell RNA-seq data of E18 fetal thymocytes from HEB Vav-iCre and Id3-KO mice and their wild type littermate counterparts
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Effects of behavioural types on the problem-solving performance of wild house mice under controlled and semi-natural conditions
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RNAseq analysis of heart samples collected from wild-type and ZNF768 null mice 8 hours post-irradiation
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The genetics of immune and infection phenotypes in wild mice, Mus musculus domesticus
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Single-Cell RNA-sequencing of neural precursor cells from an Alzheimer's mouse model, wild-type mice, and Alzheimer's mice rescued with Usp16 haploinsufficiency
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Relationships between immune gene expression and circulating cytokine levels in wild house mice
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Data from: Phenotypic resources immortalized in a panel of wild-derived strains of five species of house mice
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Data from: Sleep, inflammation, and cognitive behavior of aged wild-type mice subjected to diffuse brain injury and aged 3xTg-AD mice as a model of Alzheimer’s disease
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Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA
We examined sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 290 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified), western Europe (domesticus, DOM), and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia, and Korea, are inferred, with the possibility of several different routes.
Data from: Infection-induced behavioural changes reduce connectivity and the potential for disease spread in wild mice contact networks
Infection may modify the behaviour of the host and of its conspecifics in a group, potentially altering social connectivity. Because many infectious diseases are transmitted through social contact, social connectivity changes can impact transmission dynamics. Previous approaches to understanding disease transmission dynamics in wild populations were limited in their ability to disentangle different factors that determine the outcome of disease outbreaks. Here we ask how social connectivity is affected by infection and how this relationship impacts disease transmission dynamics. We experimentally manipulated disease status of wild house mice using an immune challenge and monitored social interactions within this free-living population before and after manipulation using automated tracking. The immune-challenged animals showed reduced connectivity to their social groups, which happened as a function of their own behaviour, rather than through conspecific avoidance. We incorporated these disease-induced changes of social connectivity among individuals into models of disease outbreaks over the empirically-derived networks. The models revealed that changes in host behaviour frequently resulted in the disease being contained to very few animals, as opposed to becoming widespread. Our results highlight the importance of considering the role that behavioural alterations during infection can have on social dynamics when evaluating the potential for disease outbreaks.
Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures
<p>Data files for Vogt et al. 2024</p>
RNA sequencing data from the prefrontal cortex and hippocampus of male (12 weeks old) hemizyguous CAG-HERV-W-env mice and wild-type controls
<p>RNA sequencing data from the prefrontal cortex (PFC) and hippocampus (HIPP) of male (12 weeks old) hemizyguous CAG<sup>HERV-Wenv </sup>mice ( C57BL6/J;129P2/Ola-Hprt mice; <em>n</em> = 3) relative to wild-type ( <em>n</em> = 3) littermates. Total RNA was extracted from prefrontal and hippocampal samples using the SPLIT RNA extraction kit (Lexogen, Austria) following the manufacturer’s recommendations and was sent to the Functional Genomics Center in Zurich (FGCZ) for quality control and RNA sequencing. The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1, a 28S/18S ratio within 1.5–2, and RIN (>8) values qualified for a Poly-A enrichment strategy in order to generate the sequencing libraries applying the TruSeq mRNA Stranded Library Prep Kit (Illumina, Inc, California, USA). After Poly-A selection using Oligo-dT beads the mRNA was reverse-transcribed into cDNA. The cDNA was fragmented, end-repaired and poly-adenylated before ligation of TruSeq UD Indices (IDT, Coralville, Iowa, USA). The quality and quantity of the amplified sequencing libraries were validated using a Fragment Analyzer SS NGS Fragment Kit (1–6000 bp) (Agilent, Waldbronn, Germany). The equimolar pool of the samples was spiked into a NovaSeq6000 run targeting ~15M reads per sample on a S1 FlowCell (Novaseq S1 Reagent Kit, 100 cycles, Illumina, Inc, California, USA). Reads were quality-checked with FastQC. Sequencing adapters were removed with Trimmomatic and aligned to the reference genome and transcriptome of Mus Musculus (GENCODE, GRCm38,p5) with STAR v2.7.3. Distribution of the reads across genomic isoform expression was quantified using the R package GenomicRanges from Bioconductor Version 3.10. Minimum mapping quality, as well as minimum feature overlaps, was set to 10. Multi-overlaps were allowed. Differentially expressed genes (DEGs) were identified using the R package edgeR from Bioconductor Version 3.10, using a generalized linear model (glm) regression, a quasi-likelihood (QL) differential expression test and the trimmed means of M-values (TMM) normalization.</p>
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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.