Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA231156 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide analysis of gene expression within vitiligo lesional skin with active inflammation
| PRJNA231158 | ENA
Project description:PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea. Keywords: other
2004-01-02 | GSE887 | GEO
Project description:Skin samples from mice in a model of vitiligo were selected for gene expression profiling in order to identify active inflammatory pathways. Total RNA isolated from 6 mouse samples from fresh skin, 3 from vitiligo mice and 3 from control mice.
2013-12-12 | E-GEOD-53147 | biostudies-arrayexpress
Project description:Vitiligo is a common autoimmune skin disorder. We constructed an induced vitiligo mouse model and performed bulk-RNA sequencing on the skin and 16S rRNA sequencing of feces from vitiligo mice and uninduced mice. Next, we performed skin bulk-RNA sequencing after treatment using ABX. Lastly, we subjected gut microbe-related metabolite hippuric acid to control mice and performed bulk-RNA sequencing on the skin to observe oxidative stress-related gene expression changes.
2024-08-21 | GSE273242 | GEO
Project description:Background: Comparison of temporal gene expression profiles. The RNA-seq data comprises 3 age groups: 2, 15 and 30 months for mouse skin; 5, 24 and 42 months for zebrafish skin. Illumina 50bp single-stranded single-read RNA sequencing Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2015-12-01 | GSE46916 | 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.
| S-EPMC8784167 | biostudies-literature
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:Vitiligo skin samples with an active inflammatory infiltrate were selected for gene expression profiling in order to identify inflammatory pathways that drive depigmentation in vitiligo. Total RNA was isolated from 10 deidentified human samples from formalin fixed, paraffin-embedded skin, 5 from vitiligo patients and 5 from controls. Control skin was age- and site-matched excision tips without pathology.
2013-12-12 | E-GEOD-53146 | biostudies-arrayexpress
Project description:To characterize the genetic basis of hybrid male sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven ‘hotspots,’ seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL - but not cis eQTL - were substantially lower when mapping was restricted to a ‘fertile’ subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility.
2014-05-01 | GSE54089 | GEO
Project description:Comparison of gene expression profiles from Mus musculus skin of two age groups. The RNA-seq data comprise 2 groups at ages: 2 and 9 months. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2021-10-19 | GSE120570 | GEO