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Single cell transcriptomic analysis of skeletal muscle cells

ABSTRACT: Single cell transcriptomic analysis of skeletal muscle cells

PROVIDER: PRJNA1037093 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26744578_1.fastq.gz	Fastqsanger.gz
	SRR26744578_2.fastq.gz	Fastqsanger.gz
	SRR26744579_1.fastq.gz	Fastqsanger.gz
	SRR26744579_2.fastq.gz	Fastqsanger.gz

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Single cell transcriptomic analysis of skeletal muscle cells

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Comparative Proteomic and Transcriptomic Analysis of Follistatin-induced Skeletal Muscle Hypertrophy

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Single-cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2-deficient vascular progenitors into skeletal muscle

Project description:An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line, in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. Unexpectedly, a cell population with a skeletal muscle signature was observed in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites, elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos.

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Single cell RNA-Seq analysis of human skeletal muscle organoids

Project description:We performed single cell RNA sequencing analysis of human iPSC-derived skeletal muscle organoids at 12 week post differentiation stage.

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Project description:This study aims to characterize the diversity of cell types in human skeletal muscle across age using two complementary technologies: single-cell and single-nucleus sequencing, which provide a comprehensive coverage of cell types in the muscle. We leveraged the aforementioned datasets to study change in cell type composition and gene expression between young (n= 8, approx. 20-40 yrs) and old (n = 9, approx. 60-80 yrs) adults, highlighting changes in the major skeletal muscle compartments, muscle satellite cells, myofiber and muscle microenvironment including stromal, immune and vascular cell types. Additionally, we generated a complementary mouse muscle aging dataset by profiling hindlimb muscles from young (n = 5, 3 months) versus old mice (n = 3, 19 months), using single-cell and single-nucleus sequencing for comparison.

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Single-cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2-deficient vascular progenitors into skeletal muscle

Project description:During vertebrate embryogenesis, vascular endothelial cells originate in the lateral plate mesoderm (LPM) next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line, in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly, a cell population with the skeletal muscle signature was observed in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites, elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors, thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally, we demonstrate that arterial progenitors co-express multiple arterial and venous markers during early stages of vasculogenesis, suggesting multi-potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular, muscle and other types of progenitors for therapeutic purposes.

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Proteogenomic single cell analysis of skeletal muscle myocytes

Project description:Background: Skeletal muscle myocytes have evolved into slow and fast-twitch types. These types are functionally distinct as a result of differential gene and protein expression. However, an understanding of the complexity of gene and protein variation between myofibers is unknown. Methods: We performed deep, whole cell, single cell RNA-seq on intact and fragments of skeletal myocytes from the mouse flexor digitorum brevis muscle. We compared the genomic expression data of 171 of these cells with two human proteomic datasets. The first was a spatial proteomics survey of mosaic patterns of protein expression utilizing the Human Protein Atlas (HPA) and the HPASubC tool. The second was a mass-spectrometry (MS) derived proteomic dataset of single human muscle fibers. Immunohistochemistry and RNA-ISH were used to understand variable expression. Results: scRNA-seq identified three distinct clusters of myocytes (a slow/fast 2A cluster and two fast 2X clusters). Utilizing 1,605 mosaic patterned proteins from visual proteomics, and 596 differentially expressed proteins by MS methods, we explore this fast 2X division. Only 36 genes/proteins were mosaic across all three studies, of which nine are newly described as variable between fast/slow twitch myofibers. An additional 414 genes/proteins were identified by two methods. Immunohistochemistry and RNA-ISH generally validated variable expression across methods presumably due to species-related differences. Conclusions: In this first integrated proteogenomic analysis of mature skeletal muscle myocytes we validate the main fiber types and greatly expand the known repertoire of twitch-type specific genes/proteins. We also demonstrate the importance of integrating genomic and proteomic datasets.

2020-01-15 | GSE143636 | GEO

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