GEO series
Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [CUT&RUN]
GSE293129
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
36 samples
Submitted 2025/11/13
Platform GPL30172
Summary
Loss of regeneration is a key feature of aging organs, often linked to stem cell exhaustion. Skeletal muscle stem cells (MuSCs) undergo age-related numerical and functional decline, contributing to reduced regenerative potential. Using low-input multi-omics, we systematically profiled the epigenome, transcriptome, and 3D genome of MuSCs from individual mice across 3 age groups (young, old, and geriatric) and both sexes. At baseline, young male MuSCs showed reduced expression of cell cycle-related mRNAs. In aged mice, particularly males, MuSCs exhibited early alterations (emerging during the transition from young to old age), including enhanced proinflammatory signaling, and loss of cell identity. Late alterations (emerging during the transition from old to geriatric age) included heightened inflammation, widespread enhancer activation, and extensive 3D genome rewiring. Proinflammatory pathways were enriched for interferon signaling and correlated with endogenous retroviral expression and NFκB activity. Late-stage epigenome and 3D genome rewiring reflected downstream degenerative changes in muscle organization, response to cytokines, and loss of myogenic identity. Thus, progressive molecular shifts may explain the aggravated proliferative deficit and functional impairment observed in MuSCs during aging.
Published in
Shi C, Yang N, Pizano E et al.
· Aging cell 2026
· PMID 41239549
· doi:10.1111/acel.70289
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE293129_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 36 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1242858 and SRA study SRP573663. Searching any of these in the dataset finder brings you back here.
Study design
36 conditions, each sampled once — no replicated groups
Read from 36 sample titles: 36 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM8877075 YM1_H3K4me1
- GSM8877076 YM2_H3K4me1
- GSM8877077 YM3_H3K4me1
- GSM8877078 YF1_H3K4me1
- GSM8877079 YF2_H3K4me1
- GSM8877080 YF3_H3K4me1
- GSM8877081 OM1_H3K4me1
- GSM8877082 OM2_H3K4me1
- GSM8877083 OM3_H3K4me1
- GSM8877084 OM4_H3K4me1
- GSM8877085 OM5_H3K4me1
- GSM8877086 OF1_H3K4me1
- GSM8877087 OF2_H3K4me1
- GSM8877088 OF3_H3K4me1
- GSM8877089 OF4_H3K4me1
- GSM8877090 GM1_H3K4me1
- GSM8877091 GM2_H3K4me1
- GSM8877092 GF1_H3K4me1
- GSM8877093 GF2_H3K4me1
- GSM8877094 YM1_H3K27ac
- GSM8877095 YM2_H3K27ac
- GSM8877096 YM3_H3K27ac
- GSM8877097 YF1_H3K27ac
- GSM8877098 YF2_H3K27ac
- GSM8877099 OM1_H3K27ac
- GSM8877100 OM2_H3K27ac
- GSM8877101 OM3_H3K27ac
- GSM8877102 OM4_H3K27ac
- GSM8877103 OF1_H3K27ac
- GSM8877104 OF2_H3K27ac
- GSM8877105 OF3_H3K27ac
- GSM8877106 GM1_H3K27ac
- GSM8877107 GM2_H3K27ac
- GSM8877108 GM3_H3K27ac
- GSM8877109 GF1_H3K27ac
- GSM8877110 GF2_H3K27ac
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