Omics Approaches to Understanding Muscle Biology

Description

Contents About the Authors Chapter 1: The Role of Omics Approaches in Muscle Research References Part I: Genomic and Epi-genomic Chapter 2: Genome-Wide Association Studies in Muscle Physiology and Disease 2.1 Historical Outline and Rationale 2.2 Outline of GWAS Methods 2.3 Applications of GWAS to Muscle Biology 2.3.1 Applications in Muscle Physiology 2.3.2 Applications in Muscle Disease 2.4 Limitations and Extensions 2.5 Future Directions References Chapter 3: Chromatin Epigenomics in Muscle Development and Disease 3.1 Introduction 3.2 Chromatin Immunoprecipitation 3.3 DamID 3.4 ATAC-seq 3.5 Limitations 3.6 Vital Future Directions References Chapter 4: Guidelines for Bioinformatics and the Statistical Analysis of Omic Data 4.1 Bioinformatics: An overview 4.2 Major Applications 4.2.1 Bioinformatics of Genomics Data 4.2.2 Other Bioinformatics Analyses 4.2.3 Platforms Used 4.2.4 Downstream Analysis and Visualization 4.2.5 Conclusion 4.3 Statistical Analysis 4.3.1 Study Design Principles 4.3.1.1 Hypothesis 4.3.1.2 Replicates 4.3.1.3 Understanding Sources of Variability 4.3.1.4 Adequate Sample Size 4.3.1.5 Data Representation 4.3.2 Statistical Analysis Methods 4.3.2.1 Data Type 4.3.2.2 Dependent Versus Independent Variables 4.3.2.3 Parametric Versus Nonparametric 4.3.2.4 Common Statistical Tests 4.3.2.5 Statistical Model Complexity 4.3.2.6 Multiple Testing 4.3.2.7 Limitations and Future Directions References Part II: Transcriptomic Chapter 5: Transcriptomic Approaches for Muscle Biology and Disorders 5.1 Theory and History of the Technique 5.2 Major Applications 5.2.1 Hybridization-Based Platforms 5.2.1.1 Affymetrix 5.2.1.2 Illumina 5.2.1.3 Agilent Technologies 5.2.2 Sequencing-Based Platforms 5.2.2.1 Illumina 5.2.2.2 Ion Torrent 5.2.2.3 Pacific Biosciences 5.2.2.4 Oxford Nanopore 5.2.3 Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) Assay 5.2.4 Single-Cell RNA Sequencing 5.3 Data Analyses 5.3.1 Microarrays 5.3.2 RNA-Sequencing (RNA-Seq) 5.3.3 Single-Cell Sequencing 5.4 Platform Selection and Limitations 5.5 Vital Future Directions References Chapter 6: Approaches to Studying the microRNAome in Skeletal Muscle 6.1 Theory and History of the Technique 6.2 Major Applications 6.2.1 miRNA Profiling 6.2.2 Sample Types and Extraction Methods 6.2.2.1 Muscle Biopsies or Whole Muscles 6.2.2.2 Muscle Cell Lines 6.2.2.3 Additional Considerations 6.2.3 Sample Heterogeneity 6.2.4 Concentration and Quality Assessment 6.2.5 miRNA Profiling Methods 6.2.6 qRT-PCR-Based Methods 6.2.7 Hybridization-Based Methods 6.2.7.1 miRNA Microarrays 6.2.7.2 NanoString nCounter Gene Expression System 6.2.8 miRNA Sequencing 6.2.9 miRNA Databases 6.3 Limitations 6.4 Vital Future Directions References Part III: Proteomic Chapter 7: Proteomic Profiling of Human Skeletal Muscle in Health and Disease 7.1 Theory and History of the Technique 7.2 Major Applications 7.3 Limitations 7.4 Vital Future Directions References Chapter 8: Proteome Profiling of Muscle Cells and Muscle Tissue Using Stable Isotope Labeling by Amino Acids 8.1 Theory and History of Stable Isotope Labeling by Amino Acids for Proteomic Studies 8.1.1 Stable Isotope Labeling by Amino Acid in Cell Culture (SILAC) 8.1.2 Stable Isotope Labeling in Mammals (SILAM) 8.2 Implementation of SILAC and SILAM Strategies to Study the Proteome of Muscle in Health and Disease Conditions 8.2.1 In Vitro Studies Using SILAC Labeled Muscle Cell Cultures 8.2.1.1 Study of Muscle Cell Differentiation and Myogenesis 8.2.1.2 Study of the Muscle Cell Secretome 8.2.2 In Vivo Studies Using SILAM Labeled Mouse Model for Muscle Diseases 8.2.2.1 Use of SILAM Strategy to Define Alterations in the Proteome of Dystrophin-Deficient Skeletal Muscle 8.2.2.2 Use of SILAM Strategy to Accurately Quantify Levels of Dystrophin Protein in Skeletal Muscle 8.2.2.3 Use of SILAM Mouse to Define Serum Protein Biomarkers Associated with Dystrophin Deficiency 8.3 Limitations and Extensions of the Technique 8.4 Vital Future Directions References Chapter 9: Investigating Muscle Protein Turnover on a Protein-by-Protein Basis Using Dynamic Proteome Profiling 9.1 Theory and History of the Technique 9.2 Major Applications 9.3 Limitations 9.4 Vital Future Directions References Part IV: Metabolomic Chapter 10: Skeletal Muscle Metabolomics for Metabolic Phenotyping and Biomarker Discovery 10.1 Theory and History of Metabolomics 10.1.1 Experimental Design 10.1.2 Sample Processing 10.1.3 Analytical Method 10.1.4 Data Preprocessing 10.1.5 Data Analysis 10.2 Major Applications 10.3 Limitations and Extensions of Metabolomics 10.4 Vital Future Directions 10.4.1 Metabolomics for Precision/Personalized Medicine 10.4.2 Predictive and Preventive Health: Supporting the Worldwide Healthcare System [123] 10.4.3 Single Muscle Fiber Metabolomics 10.4.4 Spatial Resolution in Metabolomics Experiments References