GEO DataSets

(Submitter supplied) We utilize an integrative genomics approach (bulk RNA-Seq, ATAC-Seq) to show how Muscle Stem Cells (MuSCs) from distinct age groups (young and aged) are significantly altered during the regenerative response. Transcriptional landscapes during quiescence, activation, proliferation and differentiation from young and aged mice are profiled and chromatin accessibility is compared.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

90 Samples

Download data: BIGWIG, NARROWPEAK, TAGALIGN, TSV, TXT

(Submitter supplied) Adult stem cells occupy a niche that contributes to their function but how stem cells remodel their microenvironment remains an open-ended question. Herein, biomaterials-based systems and metabolic labeling were utilized to evaluate how skeletal muscle stem cells and mesenchymal progenitors (fibro-adipogenic progenitors) deposit and remodel extracellular matrix. Differences in matrix production of muscle stem cells on substrates with different stiffness were then evaluated and linked with stem cell activation state. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: TSV

(Submitter supplied) Utilizing glycerol intramuscular injections in M. musculus provides a model of skeletal muscle damage followed by skeletal muscle regeneration. In particular, glycerol-induced muscle injury triggers accute activation of muscle Fibro/Adipogenic Progenitors, also called FAPs. However, aging dramatically impairs FAP function. We characterized genome-wide expression profiles of young and old FAPs in the non-proliferative and activated state, freshly isolated to non-injured or damaged muscles, respectively. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

24 Samples

Download data: TXT

(Submitter supplied) We report that whole body PRMT7-/- adult mice display a significant reduction in in muscle mass. RNA sequencing was performed to identify potential PRMT7 targets. We found that top canonical pathways affected by the loss of PRMT7 includes cell cycle and senescence.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: XLS

(Submitter supplied) Calcitonin receptor (CalcR) signaling is essential pathway for maintaining quiescence in muscle stem cells (Stem Cells. 2007 Oct;25(10):2448-59, Cell Rep. 2015 Oct 13;13(2):302-14). Collagen V functions as a surrogate ligand for CalcR, and Protein kinase A (PKA)-mediated Yap1 suppression serve as the downstream of CalcR in quiescent muscle stem cells (Nature. 2018 May;557(7707):714-718, Cell Rep. 2019 Nov 19;29(8):2154-2163.e5.). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL10787

20 Samples

Download data: TXT

(Submitter supplied) Background and Aims: Analysis of aging-induced impairments in satellite cells (SCs) – the stem cells of skeletal muscle that are required for its regeneration. Hox genes are known to control stem cell function and development of various tissues. Methods: We used AlfpCre mice for liver specific deletion of Trp53 in a conditional knockout mouse model to analyze liver carcinogenesis. Results: Here, we show that liver-specific deletion of p53 in mice consistently induces formation of liver carcinoma depicting bilineal differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

8 Samples

Download data: TXT

(Submitter supplied) Background and Aims: Analysis of aging-induced impairments in satellite cells (SCs) – the stem cells of skeletal muscle that are required for its regeneration. Hox genes are known to control stem cell function and development of various tissues.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) The regenerative capacity of skeletal muscle relies on muscle stem cells (MuSCs, or satellite cells) and its niche interactions with different neighboring cells. To understand the cellular diversity within adult skeletal muscle tissue, we harvested mononuclear cells from hindlimb skeletal muscles, sorted into single cells and profiled them by single-cell RNA-seq. To further understand and compare the expression profile between MuSCs and a novel smooth-muscle/mesenchymal-like cells (SMMCs) population, we isolated the two cell types by FACS and profiled them respectively by bulk RNA-seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

13 Samples

Download data: CSV, TSV

(Submitter supplied) We previously showed that STAT3 regulates myoblast differentiation in cell culture models, yet its role in adult muscle satellite cells (MuSC) in vivo was less well characterized. When Stat3 was conditionally deleted in MuSC, muscle development and adult MuSC formation were not affected. However, with repeated muscle injuries, the number of the quiescent MuSC in STAT3-null mice decreased and the regeneration was delayed, suggesting defective MuSC maintenance. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: BW, DIFF

(Submitter supplied) We utilize RNA-Seq to evaluate how loss of Sestrin1,2, a conserved set of stress-inducible proteins, alters the metabolism and quiescent state of young (2-3 months) Muscle Stem Cells (MuSCs) during the regenerative response.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TSV

(Submitter supplied) A variety of epigenetic alterations impairs functions of cells and tissues during aging, but it is not known if epigenetic alterations are associated with aging muscle. Here, we examined the changes of a panel of histone marks and found H3K27ac (an active enhancer mark) is markedly increased during aging in human skeletal muscle tissues. Our integrated analysis showed that enhancer activation during muscle aging is associated with the up-regulation of extracelluar matrix (ECM) genes, which may result in stiffness of the niche environment of satellite cells (SCs). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15103

3 Samples

Download data: BED

(Submitter supplied) During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: RDS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057

22 Samples

Download data

(Submitter supplied) To uncover new pathways that are important for skeletal muscle stem cell aging, we performed multiomics profiling, including transcriptomics, DNA methylomics, proteomics, and metabolomics on quiescent muscle stem cells from young and old mice. Our goals were to discover pathways that have been overlooked by isolated profiling approaches and to gain insight into which changes are causal, compensatory, correlational, and consequential. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) To uncover new pathways that are important for skeletal muscle stem cell (MuSC) aging, we performed multiomics profiling, including transcriptomics, DNA methylomics, proteomics, and metabolomics on quiescent MuSCs from young and old mice. Our goals were to discover pathways that have been overlooked by isolated profiling approaches and to gain insight into which changes are causal, compensatory, correlational, and consequential. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) To uncover new pathways that are important for skeletal muscle stem cell aging, we performed multiomics profiling, including transcriptomics, DNA methylomics, proteomics, and metabolomics on quiescent muscle stem cells from young and old mice. Our goals were to discover pathways that have been overlooked by isolated profiling approaches and to gain insight into which changes are causal, compensatory, correlational, and consequential. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) Adult skeletal muscle regeneration is mainly driven by muscle stem cells (MuSCs), which are highly heterogeneous. Although recent studies have started to characterize the heterogeneity of MuSCs, whether a subset of cells with distinct exists within MuSCs remains unanswered. Here, we found that a population of MuSCs, marked by Gli1 expression, is required for muscle regeneration. The Gli1+ MuSC population displayed advantages in proliferation and differentiation both in vitro and in vivo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

7 Samples

Download data: XLSX

(Submitter supplied) Successful skeletal muscle regeneration is primarily mediated by muscle stem cells or satellite cells which express Pax7. In homeostasis, these satellite cells exist in a ‘genuine quiescent’ state, although some satellite cells may also be primed. After an acute injury, satellite cells, enabled by several other niche cells in the muscle tissue, undergo a series of molecular and cellular changes such as activation, proliferation, and differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23479 GPL19057

28 Samples

Download data: ARROW, FPKM_TRACKING, RDS

(Submitter supplied) The mechanisms by which Pax7 promotes skeletal muscle stem (satellite) cell identity are not yet understood. We have taken advantage of pluripotent stem cells wherein the induced expression of Pax7 robustly initiates the muscle program and enables the generation of muscle precursors that repopulate the satellite cell compartment upon transplantation. Pax7 binding was excluded from H3K27 tri-methylated regions, suggesting that recruitment of this factor is circumscribed by chromatin state. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17021

42 Samples

Download data: BED, BIGWIG, NARROWPEAK, TXT