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Transcriptomic profiling of young and aged spermatogonial stem cells (RNA-Seq)

ABSTRACT: Spermatogonial stem cells (SSC), the foundation of spermatogenesis and male fertility, possess lifelong self-renewal activity. Aging leads to the decline in stem cell function and increased risk of paternal age-related genetic diseases. In the present study, we performed a comparative genomic analysis of mouse SSC (Oct4-GFP+/KIT-) and differentiating progenitors (Oct4-GFP+/KIT+) isolated from young and aged testes. Our transcriptome data revealed enormous complexity of expressed coding and non-coding RNAs and alternative splicing regulation during SSC differentiation. Further comparison between young and aged SSCs suggested these differentiation programs were affected by aging. We identified aberrant expression of genes associated with meiosis and TGF-β signaling , alteration in alternative splicing regulation and differential expression of specific lncRNAs such as Fendrr.

ORGANISM(S): Mus musculus

PROVIDER: GSE164604 | GEO | 2021/06/14

REPOSITORIES: GEO

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single cell RNA sequencing of hematopoietic stem cells aged in old and young niches

Project description:Purpose: Compare the transcriptome of hematopoietic stem cells (HSCs) that were aged in old and young niches Methods: barcoded GFP+ HSCs were FACS-sorted from a) three recipient mice 15 months post transplantation, and b) six serial transplantation recipient mice 5 months after the 8th transplantation, then subjected to processed using the Chromium Single-cell 3′ v2 Library Kit (10× Genomics, Pleasanton, CA) following the manufacturer’s instructions Results: we obtained transcriptomes of about 12k HSCs aged in young niche, and about 10k HSCs aged in old niche, with the average sequencing depth at close to 50k reads per cell Conclusions: we identified striking differences in gene expression profiles 1) between HSCs aged in young niches from mice with early aging and from mice with delayed aging, and 2) between HSCs aged in old niches and young niches when mice exhibited hematopoietic aging phenotype

2021-01-01 | GSE154772 | GEO

Aging of mouse spermatogonial stem cells by Wnt7b-Jnk pathway activation [ChIP-seq]

Project description:Because spermatogonial stem cells (SSCs) are virtually immortal by serial transplantation, SSC decrease in aged testes is considered to be caused by deteriorated microenvironment. Here we report cell-intrinsic mode of SSC aging. SSCs cultured for 5 years proliferate more actively than young SSCs and showed enhanced glycolytic activity but remain euploid and exhibited stable androgenetic imprinting patterns. Moreover, the aged SSCs kept constant SSC activity despite shortened telomeres. The increased proliferative activity of aged SSCs was caused by Wnt7b expression, which likely occurred due to decreased polycomb complex2 activity. Aberrant Wnt7b expression not only decreased reactive oxygen species levels and mitochondria activity but also stimulated glycolysis via c-jun N-terminal kinase (JNK) activation. Analysis of SSCs in Klotho aging mouse model also confirmed hyperactivation of JNK pathway and increased glycolysis. Therefore, not only SSC microenvironment but also intrinsic activation of Wnt7b-mediated glycolysis plays important roles in SSC aging.

2019-07-30 | GSE120777 | GEO

Aging of mouse spermatogonial stem cells by Wnt7b-Jnk pathway activation [Bisulfite-seq]

2019-07-30 | GSE120775 | GEO

RNA-seq from gastrocnemius muscles from rats aged 6, 12, 18, 21, 24 and 27 months

Project description:To gain new insights into molecular changes in skeletal muscle aging and disease with a special focus on differential alternative splicing and senescence, we performed RNA-seq on rat gastrocnemius muscles of animals aged 6, 12, 18, 21, 24 and 27 months, using a rat sarcopenia model we had previously established.

2021-06-26 | E-MTAB-10583 | biostudies-arrayexpress

Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus [ATAC-Seq]

Project description:Long-term memory formation is dependent on gene expression changes in the hippocampal region of the brain. Aging-related memory impairments and incidence of pathological memory disorders such as Alzheimer’s disease differ between males and females, and yet little is known about how aging-related changes to the transcriptome and chromatin environment differs between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus of both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response, cell adhesion, and synaptic function, and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic activity. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Overall, sex differences in both gene expression and chromatin accessibility were amplified with aging, revealing that although some aspects of hippocampal aging are sex-independent, underlying sex differences in gene expression and chromatin dynamics in aging may shed light on sex differences in aging-related and pathological memory loss.

2023-10-16 | GSE244503 | GEO

Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus [RNA-Seq 2]

2023-10-17 | GSE244505 | GEO

Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus [RNA-Seq 1]

2023-10-17 | GSE244504 | GEO

oocyte miRNA profiling by array

Project description:This study compares miRNA expression profiles in mouse oocytes as young oocytes vs aged oocytes, and growing oocytes vs small oocytes from primordial follicles. Oocytes were derived from the ovary of young (6-8 week-old) C57BL/6 mice and aged (41-43 week-old) mice and pooled according to whether they were 20 to 50 um or 60 to 80 um in diameter. Of oocytes with the diameter of more than 60um, oocyte from young mice are called ‘young oocytes’ and those from aged mice near the end of their reproductive life span are called ‘aged oocytes’ to analyze the miRNA profiling associated with aging. They were also each called ‘small oocytes’ or ‘large oocytes’ from the size of 60um so as to investigate miRNA profiling associated with growing. Total RNA from oocytes was isolated using mirVana miRNA Isolation Kit (Applied Biosystems). MiRNA expression was profiled using Agilent's Mouse miRNA Microarray Kit (G4472A) annotated against the Sanger miRBASE 10.1 database of miRNAs. This miRNA microarray was provided by Agilent Technologies (Santa Clara, CA). Each sample was run in duplicate.

2012-09-04 | E-GEOD-17966 | biostudies-arrayexpress

Tracking gene expression changes following aging of C. elegans

Project description:Track down the differential gene expressions between young and aged C. elegans to build a aging metabolism map Track down the differential gene expressions between young and aged C. elegans to build a aging metabolism map

2022-08-06 | GSE210389 | GEO

Small extracellular vesicles from young plasma reverse age-related functional declines by improving mitochondrial energy metabolism

Project description:Aging and the chronic diseases associated with aging have become a great burden to modern society. Recent animal studies on heterochronic parabiosis have revealed that young blood has a powerful rejuvenating effect on aged tissues, but which components of the young blood are responsible for the rejuvenating effects remains unclear. In this study, we found that small extracellular vesicles (sEVs) purified from the plasma of young mice could counteract pre-existing aging at the molecular, mitochondrial, cellular and physiological levels. In detail, injection of young sEVs into aged mice extended lifespan, attenuated senescent phenotypes and mitigate age-associated impairments on various tissues (hippocampus, muscle, heart, testis, bone, etc). Mechanistical studies using iTRAQ-based quantitative proteomic analyses combined with GO term cluster revealed that the altered proteomes in aged tissues of young sEVs-treated mice were specifically related to their roles in regulating cellular senescence, metabolic process, epigenetic modification, genomic stability, etc, which are the cardinal features associated with aging. Particularly, the sEVs derived from young mice and young human donors could stimulate PGC-1α (a master regulator of mitochondrial biogenesis and energy metabolism) expression in vitro and in vivo through their rejuvenating miRNA cargos, thereby facilitating mitochondrial regeneration and counteracting mitochondrial deficits in aged tissues. Taken together, this study demonstrates that young sEVs can reverse degenerative changes and age-related dysfunctions through stimulating PGC-1α expression and regenerating intact mitochondria.

2024-03-31 | PXD030350 | Pride

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