Mus pahari
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1215677 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed RNA-seq experiments Mus caroli and Mus pahari to aid in annotating their genomes. RNA was extracted from multiple tissues: brain, liver, heart and kidney. Complementary ChIP-seq data in this study have also been deposited in ArrayExpress, under accesison number E-MTAB-5769 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5769/ )
2018-03-06 | E-MTAB-5768 | biostudies-arrayexpress
Project description:RNA-seq analysis of Mus caroli and Mus pahari
| PRJEB20980 | ENA
Project description:This project aims to sequence ands denovo assemble Mus pahari genomes
| PRJEB9275 | ENA
Project description:We explored the microevolutionary trends of CTCF binding evolution by preforming ChIP-seq experiments in five closely related Mus strains, subspecies and species: Mus musculus domesticus, Mus musculus castaneus, Mus spretus, Mus caroli and Mus pahari. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. Complementary RNA-seq data from this same study have been deposited in ArrayExpress under accession numebr E-MTAB-5768 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5768 ).
2018-03-06 | E-MTAB-5769 | biostudies-arrayexpress
Project description:Mus pahari is a wild-derived, inbred mouse strain. M. pahari colony managers observed fragility of this strain's skin resulting in separation of tail skin from the mouse if handled incorrectly. Tail skin tension testing of M. pahari resulted in significantly lowered force threshold for caudal skin rupture and loss in comparison to closely related inbred mouse species and subspecies and even more than a model for junctional epidermolysis bullosa. Histologically, the tail skin separated at the subdermal level with the dermis firmly attached to the epidermis, excluding the epidermolysis bullosa complex of diseases. The dermal collagen bundles were abnormally thickened and branched. Elastin fiber deposition was focally altered in the dermis adjacent to the hair follicle. Collagens present in the skin could not be differentiated between the species in protein gels following digestion with pepsin. Together these data suggest that M. pahari have altered extracellular matrix development resulting in separation of the skin below the level of the dermis with moderate force similar to the African spiny mouse (Acomys spp.).
| S-EPMC5331852 | biostudies-literature
Project description:RNA sequencing of Mus musculus thymic lymphomas
2019-06-06 | GSE85894 | GEO
Project description:Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
| S-EPMC5880236 | biostudies-literature
Project description:RNA sequencing of Mus musculus thymic lymphomas
2020-12-30 | GSE121739 | GEO