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Mus musculus strain:C57 BL/6J

ABSTRACT: Bacterial microbiota analysis of mice

PROVIDER: PRJDB14669 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	DRR414700_1.fastq.gz	Fastqsanger.gz
	DRR414700_2.fastq.gz	Fastqsanger.gz
	DRR414701_1.fastq.gz	Fastqsanger.gz
	DRR414701_2.fastq.gz	Fastqsanger.gz
	DRR414702_1.fastq.gz	Fastqsanger.gz

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Characterizing phenotypic data of Peromyscus leucopus compared to C57BL/6J Mus musculus and diversity outbred (DO) Mus musculus.

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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Mus musculus strain:C57 BL/6J

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Mus musculus strain:C57 BL/6J

Project description:Mus musculus strain:C57 BL/6J Epigenomics

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Mus musculus strain:C57 BL/6J

Project description:Mus musculus strain:C57 BL/6J Transcriptome or Gene expression

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Mus musculus strain:C57 BL/6J

Project description:Single Zygote RNA sequencing

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Mus musculus strain:C57 BL/6J

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Mus spretus LINE-1s in the Mus musculus domesticus inbred strain C57BL/6J are from two different Mus spretus LINE-1 subfamilies.

Project description:A LINE-1 element, LIC105, was found in the Mus musculus domesticus inbred strain, C57BL/6J. Upon sequencing, this element was found to belong to a M. spretus LINE-1 subfamily originating within the last 0.2 million years. This is the second spretus-specific LINE-1 subfamily found to be represented in C57BL/6J. Although it is unclear how these M. spretus LINE-1s transferred from M. spretus to M. m. domesticus, it is now clear that at least two different spretus LINE-1 sequences have recently transferred. The limited divergence between the C57BL/6J spretus-like LINE-1s and their closest spretus ancestors suggests that the transfer did not involve an exceptionally long lineage of sequential transpositions.

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Mus musculus strain:C57/BL | isolate:DBA | breed:C57/BL

Project description:Raw WGBS reads of mice zygotes

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Whole ganglia RNA sequencing of C57 BL/6J mice

Project description:The study goal is to identify the gene expression profile of iBAT-related ganglia (SG/T1 & T3) and iWAT-related ganglia (T13/L1 & L2). RNA sequencing demonstrated clear separation of gene expression between brown adipose tissue related ganglia (SG and T3) and white adipose tissue related ganglia (T13/L1 and L2). Each sample type also showed clear separation from each other. No significant separation was observed in different genders.

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Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SNP analysis.

Project description:MSM/Ms is an inbred strain derived from the Japanese wild mouse, Mus musculus molossinus. It is believed that subspecies molossinus has contributed substantially to the genome constitution of common laboratory strains of mice, although the majority of their genome is derived from the west European M. m. domesticus. Information on the molossinus genome is thus essential not only for genetic studies involving molossinus but also for characterization of common laboratory strains. Here, we report the construction of an arrayed bacterial artificial chromosome (BAC) library from male MSM/Ms genomic DNA, covering approximately 1x genome equivalent. Both ends of 176,256 BAC clone inserts were sequenced, and 62,988 BAC-end sequence (BES) pairs were mapped onto the C57BL/6J genome (NCBI mouse Build 30), covering 2,228,164 kbp or 89% of the total genome. Taking advantage of the BES map data, we established a computer-based clone screening system. Comparison of the MSM/Ms and C57BL/6J sequences revealed 489,200 candidate single nucleotide polymorphisms (SNPs) in 51,137,941 bp sequenced. The overall nucleotide substitution rate was as high as 0.0096. The distribution of SNPs along the C57BL/6J genome was not uniform: The majority of the genome showed a high SNP rate, and only 5.2% of the genome showed an extremely low SNP rate (percentage identity = 0.9997); these sequences are likely derived from the molossinus genome.

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