GEO DataSets

(Submitter supplied) Skeletal muscle regeneration is driven by the interaction of myogenic and non-myogenic cells. In aging, regeneration is impaired due to various dysfunctions of myogenic and non-myogenic cells, but this is not understood comprehensively. We collected an integrated atlas of 273,923 single-cell transcriptomes from muscles of young, old, and geriatric mice (4, 20, 26 months-old) at six time-points following myotoxin injury. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

32 Samples

Download data: MTX, TAR, TSV

(Submitter supplied) We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

21 Samples

Download data: CSV, ZIP

(Submitter supplied) We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium v3 platform.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: TXT

(Submitter supplied) Skeletal muscle function and regenerative capacity decline during aging, yet factors driving these changes are incompletely understood. Muscle regeneration requires temporally coordinated transcriptional programs to drive myogenic stem cells to activate, proliferate, fuse to form myofibers, and to mature myonuclei, restoring muscle function after injury. We assessed global changes in myogenic transcription programs distinguishing muscle regeneration in aged mice from young mice by comparing pseudotime trajectories from single-nucleus RNA sequencing of myogenic nuclei. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL19057

13 Samples

Download data: H5

(Submitter supplied) We report a series of spatial transcriptomics datasets of regenerating mouse muscle tissue generated with the 10x Genomics Visium platform.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: CSV, JSON, TAR, TIFF

(Submitter supplied) A new sorting protocol was used to identify and isolate different senescent cell types from damaged muscles of young and geriatric mice. Analysis revealed conservation of two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time, and aging, while cell identity traits were preserved. Senescent cells create an “aged-like” inflamed niche, mirroring inflammation-associated with aging (inflammaging), that arrests stem cell proliferation and regeneration.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28330

8 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; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28330 GPL17021 GPL24247

179 Samples

Download data

(Submitter supplied) A new sorting protocol was used to identify and isolate different senescent cell types from damaged muscles of young and geriatric mice. Analysis revealed conservation of two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time, and aging, while cell identity traits were preserved. Senescent cells create an “aged-like” inflamed niche, mirroring inflammation-associated with aging (inflammaging), that arrests stem cell proliferation and regeneration.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

69 Samples

Download data: TXT

(Submitter supplied) A new sorting protocol was used to identify and isolate different senescent cell types from damaged muscles of young and geriatric mice. Analysis revealed conservation of two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time, and aging, while cell identity traits were preserved. Senescent cells create an “aged-like” inflamed niche, mirroring inflammation-associated with aging (inflammaging), that arrests stem cell proliferation and regeneration.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

102 Samples

Download data: TXT

(Submitter supplied) We report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

5 Samples

Download data: TXT

(Submitter supplied) Adult muscle stem cells show a high transcriptional and clonal heterogeneity during ageing. Whether microRNAs contribute to this diversity is not known. Here we use tissue-specific genetic deletion of microRNA (miR)-501 that is highly enriched in activated myogenic progenitor cells to address this question. Single-cell sequencing revealed a novel subpopulation of committed myogenic progenitor cells in miR-501 knockout mice that express high levels of terminal differentiation markers and inflammatory genes such as CD74. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: MTX, TSV

(Submitter supplied) Adult muscle stem cells show a high transcriptional and clonal heterogeneity during ageing. Whether microRNAs contribute to this diversity is not known. Here we use global and tissue-specific genetic deletion of microRNA (miR)-501 that is highly enriched in activated myogenic progenitor cells 3 to address this question. Deletion of miR-501 reduced myofiber size and resilience of muscle fibers to injury and exercise in adult skeletal muscle. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28457

10 Samples

Download data

(Submitter supplied) Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

7 Samples

Download data: MTX, TSV

(Submitter supplied) Cellular senescence is the irreversible arrest of normally dividing cells and is driven by the cell cycle inhibitors Cdkn2a, Cdkn1a, and Trp53. Senescent cells are implicated in chronic diseases and tissue repair through their increased secretion of proinflammatory factors known as the senescence-associated secretory phenotype (SASP). Here, we use spatial transcriptomics and single-cell RNA sequencing (scRNAseq) to demonstrate that cells displaying senescent characteristics are “transiently" present within regenerating skeletal muscle and within the muscles of D2-mdx mice, a model of Muscular Dystrophy. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1 Sample

Download data: H5AD, TAR

(Submitter supplied) Cellular senescence is the irreversible arrest of normally dividing cells and is driven by the cell cycle inhibitors Cdkn2a, Cdkn1a, and Trp53. Senescent cells are implicated in chronic diseases and tissue repair through their increased secretion of proinflammatory factors known as the senescence-associated secretory phenotype (SASP). Here, we use spatial transcriptomics and single-cell RNA sequencing (scRNAseq) to demonstrate that cells displaying senescent characteristics are “transiently" present within regenerating skeletal muscle and within the muscles of D2-mdx mice, a model of Muscular Dystrophy. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: RDS, TAR

(Submitter supplied) As a part of the skeletal system, bone marrow environment also performs vital functions in maintaining the bone homeostasis. To gain an insight into the bone marrow environment change after osteocyte ablation, single cell RNA sequencing (scRNA-seq) was performed

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV

(Submitter supplied) To understand the mechanism underlying the bone phenotype in osteocytes ablation mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: XLSX

(Submitter supplied) Skeletal muscle stem cells are essential to muscle homeostasis and regeneration after injury. An attractive approach to obtain these cells is via differentiation of pluripotent stem cells (PSCs). We have recently reported that teratomas derived from mouse PSCs are a rich source of skeletal muscle stem cells. Here, we showed that the teratoma formation method is also capable of producing skeletal myogenic progenitors from human PSCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: MTX, TSV