Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA304429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2966660_1.fastq.gz | Fastqsanger.gz | |||
| SRR2966660_2.fastq.gz | Fastqsanger.gz | |||
| SRR2966670_1.fastq.gz | Fastqsanger.gz | |||
| SRR2966670_2.fastq.gz | Fastqsanger.gz | |||
| SRR2966661_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
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Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 5,264 nuclei in mouse adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
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Project description:In mammals, retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals after an insult or disease, some vertebrates, including zebrafish, have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic-like process in mammals’ eyes caused by differential activation of canonical and non-canonical TGFβ signaling pathways.
2019-11-03 | GSE132140 | GEO
Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
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Project description:Sigurdsson2010 - Genome-scale metabolic model
of Mus Musculus (iMM1415)
This model is described in the article:
A detailed genome-wide
reconstruction of mouse metabolism based on human Recon 1.
Sigurdsson MI, Jamshidi N,
Steingrimsson E, Thiele I, Palsson BØ.
BMC Syst Biol 2010; 4: 140
Abstract:
BACKGROUND: Well-curated and validated network
reconstructions are extremely valuable tools in systems
biology. Detailed metabolic reconstructions of mammals have
recently emerged, including human reconstructions. They raise
the question if the various successful applications of
microbial reconstructions can be replicated in complex
organisms. RESULTS: We mapped the published, detailed
reconstruction of human metabolism (Recon 1) to other mammals.
By searching for genes homologous to Recon 1 genes within
mammalian genomes, we were able to create draft metabolic
reconstructions of five mammals, including the mouse. Each
draft reconstruction was created in compartmentalized and
non-compartmentalized version via two different approaches.
Using gap-filling algorithms, we were able to produce all
cellular components with three out of four versions of the
mouse metabolic reconstruction. We finalized a functional model
by iterative testing until it passed a predefined set of 260
validation tests. The reconstruction is the largest, most
comprehensive mouse reconstruction to-date, accounting for
1,415 genes coding for 2,212 gene-associated reactions and
1,514 non-gene-associated reactions.We tested the mouse model
for phenotype prediction capabilities. The majority of
predicted essential genes were also essential in vivo. However,
our non-tissue specific model was unable to predict gene
essentiality for many of the metabolic genes shown to be
essential in vivo. Our knockout simulation of the lipoprotein
lipase gene correlated well with experimental results,
suggesting that softer phenotypes can also be simulated.
CONCLUSIONS: We have created a high-quality mouse genome-scale
metabolic reconstruction, iMM1415 (Mus Musculus, 1415 genes).
We demonstrate that the mouse model can be used to perform
phenotype simulations, similar to models of microbe metabolism.
Since the mouse is an important experimental organism, this
model should become an essential tool for studying metabolic
phenotypes in mice, including outcomes from drug screening.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180055.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180055 | BioModels
Project description:Age-associated DNA methylation increases in mouse pancreatic islets suggest an epigenetic drift toward the exocrine pancreas epigenome
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Project description:Translational research is commonly performed in the C57B6/J mouse strain, chosen for its genetic homogeneity and phenotypic uniformity. Here, we evaluate the suitability of the white-footed deer mouse (Peromyscus leucopus) as a model organism for aging research, offering a comparative analysis against C57B6/J and diversity outbred (DO) Mus musculus strains. Our study includes comparisons of body composition, skeletal muscle function, and cardiovascular parameters, shedding light on potential applications and limitations of P. leucopus in aging studies. Notably, P. leucopus exhibits distinct body composition characteristics, emphasizing reduced muscle force exertion and a unique metabolism, particularly in fat mass. Cardiovascular assessments showed changes in arterial stiffness, challenging conventional assumptions and highlighting the need for a nuanced interpretation of aging-related phenotypes. Our study also highlights inherent challenges associated with maintaining and phenotyping P. leucopus cohorts. Behavioral considerations, including anxiety-induced responses during handling and phenotyping assessment, pose obstacles in acquiring meaningful data. Moreover, the unique anatomy of P. leucopus necessitates careful adaptation of protocols designed for Mus musculus. While showcasing potential benefits, further extensive analyses across broader age ranges and larger cohorts are necessary to establish the reliability of P. leucopus as a robust and translatable model for aging studies.
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Project description:Analysis of gene expression profiles is an attractive method for discovering how animals respond to environmental challenges in nature. Compared to low altitudes, high altitudes are characterized by reduced partial pressures of oxygen (hypoxia) and cooler ambient temperatures To better understand how mammals cope with high altitudes, we trapped wild house mice (Mus musculus domesticus) from 3 populations in La Paz, Bolivia (3000 - 3600 m) and 3 populations in Lima, Peru (0 – 200 m). Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays were use to measure mRNA abundance in the livers of these mice.
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