GEO DataSets

(Submitter supplied) The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

4 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) We report the application of single myofiber ATAC-Seq (smfATAC-Seq) to investigate the chromatin accessibility of a single myofiber without the presence of confounding muscle resident cell types. This method demonstrates that open chromatin regions of myonuclei can be tagmentated and high-quality sequencing ready libraries can be generated from these fragments. To perform comparative analysis as well as to demonstrate the applicability of the smfATAC-Sew to study changes in chromatin of myonuclei within different contexts, smfATAC-Seq was performed both on uninjured myofibers as well as injured myofibers seven days after induced injury. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

13 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL24247

38 Samples

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

(Submitter supplied) The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

21 Samples

Download data: TSV

(Submitter supplied) The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

7 Samples

Download data: MAT, TXT

(Submitter supplied) The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: CSV, TXT

(Submitter supplied) We developed a method of combining single myofiber isolation with SMART-seq to analyze the whole transcriptome of single myofibers. Here we apply this technique to analyze the variation in the transcriptome of young (4 weeks) and old (19 months) mice. We see the deregulation of a variety of genes that have been reported, or may cause, the deterioration of the muscle in aging. This confirms the applicability of our novel technique for use in analyzing the transcriptome of individual myofibers under various different conditions.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

17 Samples

Download data: CSV, TAB

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

Organism:

Sus scrofa

Type:

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

Platform:

GPL26351

14 Samples

Download data: BED, MTX, TSV

(Submitter supplied) To investigate the upstream regulatory networks in myogenesis that lead to the establishment of the myogenic lineage and subsequent differentiation, we proformed scATAC-seq of pig somite and myotome cells from Tibetan pigs (ZZ) and Duroc×Tibetan pigs (DZ) at several embryonic stages (E18, E21, and E28).

Organism:

Sus scrofa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26351

6 Samples

Download data: BED, MTX, TSV

(Submitter supplied) To investigate the upstream regulatory networks in myogenesis that lead to the establishment of the myogenic lineage and subsequent differentiation, we proformed scRNA-seq of pig somite and myotome cells from Tibetan pigs (ZZ) and Duroc×Tibetan pigs (DZ) at several embryonic stages (E16, E18, E21, and E28).

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

8 Samples

Download data: MTX, TSV

(Submitter supplied) Skeletal muscle is a heterogeneous tissue. Individual myofibers that make up the contractile muscle tissue exhibit variation in their metabolic and contractile properties. Although there are biochemical and histological assays to study myofiber heterogeneity, methods to analyze the transcriptomes of individual myofibers are lacking.  We have developed single myofiber RNA-Seq (smfRNA-Seq) to analyze the whole transcriptome of an individual myofiber by combining single fiber isolation with Switching Mechanisms at 5’ end of RNA Template (SMART) technology. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV

(Submitter supplied) Voluntary exercise enhances old skeletal muscle stem cell (MuSC) function in vivo and ex vivo, dependent on upregulation of Ccnd1. To determine the transcriptional changes associated with these phenotypes, RNA-Seq was performed on MuSCs from young and old mice that had exercised or not exercised, and from young mice with MuSC-specific loss-of-function deletions in zero, one, or both alleles of Ccnd1.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

36 Samples

Download data: TXT

(Submitter supplied) ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterine endometrium. Here we show that monoallelic loss of ARID1A in the mouse endometrial epithelium is sufficient for vaginal bleeding when combined with PI3K activation. Sorted mutant epithelial cells display gene expression and promoter chromatin signatures associated with epithelial-to-mesenchymal transition (EMT). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: BROADPEAK, TXT

(Submitter supplied) ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterine endometrium. Here we show that monoallelic loss of ARID1A in the mouse endometrial epithelium is sufficient for vaginal bleeding when combined with PI3K activation. Sorted mutant epithelial cells display gene expression and promoter chromatin signatures associated with epithelial-to-mesenchymal transition (EMT). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: CSV, TAB

(Submitter supplied) ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterine endometrium. Here we show that monoallelic loss of ARID1A in the mouse endometrial epithelium is sufficient for vaginal bleeding when combined with PI3K activation. Sorted mutant epithelial cells display gene expression and promoter chromatin signatures associated with epithelial-to-mesenchymal transition (EMT). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: BROADPEAK

(Submitter supplied) ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterine endometrium. Here we show that monoallelic loss of ARID1A in the mouse endometrial epithelium is sufficient for vaginal bleeding when combined with PI3K activation. Sorted mutant epithelial cells display gene expression and promoter chromatin signatures associated with epithelial-to-mesenchymal transition (EMT). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: BROADPEAK, TXT

(Submitter supplied) ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterine endometrium. Here we show that monoallelic loss of ARID1A in the mouse endometrial epithelium is sufficient for vaginal bleeding when combined with PI3K activation. Sorted mutant epithelial cells display gene expression and promoter chromatin signatures associated with epithelial-to-mesenchymal transition (EMT). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV, TAB

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL18573 GPL19057

51 Samples

Download data: BROADPEAK, TAB

(Submitter supplied) The goal of this study was to investigate the transcriptional regulation in cells grown on Fibronectin when compared to Collagen I

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL