Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA107455 | ENA |
REPOSITORIES: ENA
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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:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis
2018-08-02 | MSV000082680 | GNPS
Project description:A transcriptome study in mouse hematopoietic stem cells was performed using a sensitive SAGE method, in an attempt to detect medium and low abundant transcripts expressed in these cells. Among a total of 31,380 unique transcript, 17,326 (55%) known genes were detected, 14,054 (45%) low-copy transcripts that have no matches to currently known genes. 3,899 (23%) were alternatively spliced transcripts of the known genes and 3,754 (22%) represent anti-sense transcripts from known genes.
2009-05-20 | GSE16139 | GEO
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:mRNA expression profiles in androgenetic, parthenogenetic and fertilized embryonic stem cells
| PRJNA196171 | ENA
Project description:Background:Maternal mRNAs that accumulate in the oocyte during oogenesis play important roles during initial stages of embryonic development, before activation of the embryonic genome. Parthenogenesis of mammalian is a critical research modle for the function analysis of maternal genomics. Results:Here we report comprehensive maternal transcriptome dynamics of single matured oocytes and pre-implantation embryos of buffalo parthenogenesis.Notably, more than half of the estimated 28659 bovine genes,15331 involved in more than 280 pathways, is expressed in oocytes and early embryos of parthenogenesis .The total numbers of genes expressed across stages are from 908 genes (morula/16cells)to 2603 genes(blastocyst/morula), and the nature of the expressed genes is also greatly different. A total of 3567 unique genes were identified to be differentially expressed between all consecutive stages of development(FPKM>0),of which the biggest expressed change was detected between the 8-and 16-cell stages, which demonstrated that parthenogenetic activation of embryonic development exist an embryonic genome activation process which is the same as the normal fertilization of embryos,also occurs between 8cells-16cells, consistent with the time of the development of the normal fertilized embryonic development,which suggesting that parthenogenetic embryonic development and normal fertilization embryo development may have a similar genome activation transcription regulation process.Besides,2726 genes were identified as only expressed/highly enriched in particular stages of development, suggesting their stage-specific roles in maternal genome during embryogenesis.Using weighted gene co-expression network analysis, we found 11 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified 1530 hub genes of the maternally expressed gene networks. Methods:Maternal mRNA profiles of pre-implantation development in buffalo parthenogenesis,using single-cell RNA sequencing in IlluminaHiSeq platform. Sequencing adapters were trimmed using Cutadapt (https://code.google.com/p/cutadapt/) and the filtered reads were mapped to the reference genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/471/725/GCA_000471725.1_UMD_CASPUR_WB_2.0/)assembly using Tophat2 followed by Cufflinks.qRT–PCR validation was performed using SYBR Green assays. Conclusions:This study provides a comprehensive examination of maternally expressed gene activities in buffalo oocytes and pre-implantation embryos of parthenogenesis for the first time,and find the special “EGA”between 8cells-16cells for parthenogenetic embry,and the study screen a number of specific stages hub gene with potentially important function.
2018-12-26 | GSE108578 | GEO