Dataset Information

The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus

ABSTRACT: This project aims to determine how genetic modifiers of normal cognitive aging impact cognitive, neurophysiological, and neurodegenerative changes in Alzheimer's disease models. Genetic variants in the BXD mouse model modulate the penetrance of 5XFAD mutations on the development and progression of cognitive defects. 40 strains from the BXD family of both males and females were collected from 6 months to 2 years of age and hippocampus tissue was collected for omics analysis.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Hippocampus

SUBMITTER: Evan Williams

LAB HEAD: Catherine Kaczorowski

PROVIDER: PXD012044 | Pride | 2026-01-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	A_SAMPLE_LIST.xlsx	Xlsx
	Library_PanMouse_v3_ForEvosep_WithDecoys.TraML	Other
	Sample_Output.csv	Csv
	combined_iRT_CiRT_201804.TraML	Other
	wevan_K181203_Inject001_SampleID_MIX.wiff	Wiff

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Project description:We used 8 strains the BXD mouse genetic reference population, including parents C57BL/6J and DBA/2J, to study the proteome of the heart, whole brain, liver, quadriceps, and brown adipose tissue (BAT) across 8 different genotypes. For each sample, we examined the proteome of the mitochondria, as well as the whole cell fraction (including mitochondria). Later, we supplemented this study with an additional 19 strains of BXD mouse, with one strain overlapping, in the BAT for both whole cell and mitochondrial extract to examine tissue-specific hypotheses generated from the original set of 8 strains. All together, these data allowed us to (1) examine proteome expression of the mitochondria, (2) examine differences in proteome expression across tissue, (3) examine differences in proteome expression across strain, and (4) examine all three of the preceding factors simultaneously against one-another. This allowed us to uncover several proteins which are expressed in the mitochondria but are not reported as such in the literature, of which we validated a few by traditional staining techniques. Furthermore, we compare our proteome data against transcriptome data gathered in the same individual mice. We observe (1) that differences in expression of genes involved in oxidative phosphorylation are far more tissue-dependent at the protein level than the transcript level, and (2) and we observe that the phenotypic relationship between BAT and thermogenesis is far more evident at the protein expression data than it is from the transcript expression. Together, these data provide two conclusions: (1) next-gen mass spectrometry proteomics techniques can identify organelle localizations that were not evident from other techniques (perhaps particularly those proteins which are expressed both inside and outside the mitochondria); and (2) proteome and transcriptome data are complimentary, and proteome data may help us find and test new hypotheses even for physiological pathways which have been well studied at the genetic and transcriptomic levels.

Dataset Information

The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus

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