Neural regulation of differentiation of rat skeletal muscle cell types

1992 ◽  
Vol 97 (6) ◽  
pp. 479-486 ◽  
Author(s):  
G. K. Dhoot
Keyword(s):  
Skeletal Muscle ◽  
Muscle Cell ◽  
Cell Types ◽  
Skeletal Muscle Cell ◽  
Neural Regulation ◽  
Rat Skeletal Muscle

scholarly journals Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

2021 ◽  
Author(s):  
Peter Orchard ◽  
Nandini Manickam ◽  
Christa Ventresca ◽  
Swarooparani Vadlamudi ◽  
Arushi Varshney ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Cell ◽  
Muscle Fiber ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Skeletal Muscle Cell ◽  
Rna Seq ◽  
Rat Skeletal Muscle ◽  
Integrative Analyses ◽  
Single Nucleus

Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell–specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site–distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome-wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (∼3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.

scholarly journals Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

2020 ◽  
Author(s):  
Peter Orchard ◽  
Nandini Manickam ◽  
Arushi Varshney ◽  
Vivek Rai ◽  
Jeremy Kaplan ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Cell ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Skeletal Muscle Cell ◽  
Type Ii ◽  
Rna Seq ◽  
Rat Skeletal Muscle ◽  
Integrative Analyses ◽  
Single Nucleus

AbstractBackgroundSkeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases, mobility, and quality of life. It is composed of several different cell and muscle fiber types.ResultsHere, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 30,531 nuclei, representing 11 libraries, profiled in this study, and identify seven distinct cell types ranging in abundance from 63% (type II fibers) to 0.9% (muscle satellite cells) of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (∼3% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, and transcription factor motifs for creatinine levels and type 2 diabetes signals.ConclusionsThese chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for investigating specific cell types and nominating causal GWAS SNPs and cell types.

Specific effect of corticoids on acetylcholine receptor expression in rat skeletal muscle cell cultures

1992 ◽  
Vol 31 (2) ◽  
pp. 285-293 ◽  
Author(s):  
J.-T. Vilquin ◽  
S. Braun ◽  
P. Labouret ◽  
G. Zuber ◽  
C. Tranchant ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Acetylcholine Receptor ◽  
Muscle Cell ◽  
Cell Cultures ◽  
Specific Effect ◽  
Skeletal Muscle Cell ◽  
Receptor Expression ◽  
Rat Skeletal Muscle
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