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Mus musculus strain:C57BL/6J

ABSTRACT: CD8+ T cell receptor (TCR) repertoire analysis

PROVIDER: PRJDB10857 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	DRR261207_1.fastq.gz	Fastqsanger.gz
	DRR261207_2.fastq.gz	Fastqsanger.gz
	DRR261208_1.fastq.gz	Fastqsanger.gz
	DRR261208_2.fastq.gz	Fastqsanger.gz
	DRR261209_1.fastq.gz	Fastqsanger.gz

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

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Mus musculus primary CD4+ T cell di-glycine remnant and whole cell proteomics

Project description:It is known that ubiquitination is important for T cell receptor (TCR) signaling during T cell activation but the breadth of ubiquitination events triggered during TCR signaling is not completely understood. This dataset utilizes di-glycine remnant profiling combined with mass spectrometry to identify a global landscape of ubiquitination events downstream of the TCR and to quantify changes ubiquitin abundance in response to TCR stimulation. Additionally, whole cell proteomics data were generated to measure protein abundances during TCR stimulation. Mouse primary T cells were isolated, proliferated and either remained resting or stimulated with CD3/CD28 to activate downstream signaling through the TCR and co-stimulatory pathways. Di-glycine remnant profiling and whole cell proteomics was performed on rested cells and cells that had undergone CD3/CD28 TCR stimulation for 4 hours. These data were analyzed to identify the ubiquitination events during TCR activation and to quantify the change in peptide-based ubiquitin abundance and total protein abundance over the course of the 4 hour TCR stimulation. Integration of di-glycine and whole cell proteomics was used to generate protein-specific predictions of whether ubiquitination events downstream of TCR signaling lead to a decrease in associated protein abundance. The analysis of these data suggests that T cell activation leads to an increase in ubiquitination that is not associated with proteasomal or lysosomal degradation.

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Project description:Deep sequencing analysis of the thymoproteasome-dependent CD8+ TCR repertoire

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Mus musculus strain:C57BL/6

Project description:Mus musculus TCR beta repertoire

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Mus musculus breed:C57BL/6J

Project description:mouse CD4+ CD8+ T cell Transcriptome

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Mus musculus breed:C57BL/6

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Mus musculus strain:C57BL/6J

Project description:Sequencing of CD8 T cell subsets from LCMV Armstrong infection

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