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Series GSE214046 Query DataSets for GSE214046
Status Public on Feb 02, 2023
Title Three-dimensional chromatin re-organization during muscle stem cell aging [scATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world’s population continues to increase. A critical contributor to sarcopenia is the loss in the number and function of muscle stem cells, which maintain tissue homeostasis and regenerate damage. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
Overall design Age-matched Hi-C and single-cell ATAC-seq (scATAC-seq) datasets from young (3 months) and aged (24-29 months) mice. Hi-C datasets were generated from muscle stem cells that were FACS-isolated from skeletal hindlimb muscles. scATAC-seq datasets were generated from single nuclei collected from skeletal hindlimb muscles.
Contributor(s) Yang BA, Aguilar C
Citation(s) 36727578
Submission date Sep 23, 2022
Last update date Feb 03, 2023
Contact name Carlos Andres Aguilar
Organization name University of Michigan, Ann Arbor
Department Biomedical Engineering
Lab Aguilar Lab
Street address 2800 Plymouth Rd
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM6598198 Young, replicate 1, scATAC-seq
GSM6598199 Young, replicate 2, scATAC-seq
GSM6598200 Aged, replicate 1, scATAC-seq
This SubSeries is part of SuperSeries:
GSE214047 Three-dimensional chromatin re-organization during muscle stem cell aging
BioProject PRJNA883691

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Supplementary file Size Download File type/resource
GSE214046_RAW.tar 5.9 Gb (http)(custom) TAR (of TBI, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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