Handbook of Translational Transcriptomics

ContributorsAcknowledgments1. Past, current, and future of transcriptomicsXinmin Li, Ilya Belalov, and Anton Buzdin1.1 Introduction1.2 Historical development1.3 Methodological advancements1.4 Microarrays1.5 RNA sequencing (RNA-seq)1.6 Single-cell RNA sequencing (scRNA-seq)1.7 Spatial transcriptomics1.8 Noncoding RNAs in gene regulation1.9 MicroRNAs (miRNAs)1.10 Long noncoding RNAs (lncRNAs)1.11 Regulatory networks1.12 Single-cell and spatial transcriptomics in understanding cellular heterogeneity1.13 Single-cell transcriptomics1.14 Spatial transcriptomics1.15 Insights and applications1.16 Challenges and future directions1.17 Emerging trends and future directions in transcriptomics1.18 RNA sequencing (RNA-seq) and beyond1.19 Dual RNA-seq for host-pathogen interactions1.20 Transcriptomics in food microbiology and agriculture1.21 Multi-omics integration1.22 Single-cell transcriptomics1.23 Challenges and future prospects1.24 Current challenges and controversies in transcriptomics1.25 Technical limitations and data complexity1.26 Interpretation of dual RNA-seq data1.27 Environmental influences on transcriptomic profiles1.28 Transcriptomics in food microbiology and safety1.29 Toxicogenomics and risk assessment1.30 Functional annotation and novel transcripts1.31 ConclusionReferences2. Pitfalls of transcriptomics and selection of the most appropriate transcriptomic techniqueXinmin Li, Ilya Belalov, and Anton Buzdin2.1 Introduction2.2 Pitfalls in specific transcriptomic techniques2.3 Choosing the right tool for the job2.4 Case studies and examples2.5 Addressing pitfalls and challenges: Insights from recent research2.6 Future directions in transcriptomics2.7 Practical considerations and conclusionReferencesFurther reading3. Bulk RNA sequencing in wet labAnton Buzdin, Ilya Belalov, Maria Suntsova, and Xinmin Li3.1 Introduction to bulk RNA sequencing3.2 Fundamental principles of bulk RNA sequencing3.3 Key technologies and methodologies in bulk RNA sequencing3.4 Sample collection and storage3.5 RNA extraction and purification3.6 Quality control measures3.7 Library preparation for bulk RNA sequencing3.8 Early barcoding and cost efficiency3.9 Direct RNA isolation strategies3.10 Sequencing platforms and technologies3.11 RNA sequencing protocols3.12 Overview of advanced RNA sequencing protocols3.13 Reagents and equipment for bulk RNA sequencing3.14 Technical and analytical quality control in RNA sequencing3.15 Bioinformatics and data analysis3.16 Data preprocessing and normalization methods for bulk RNA sequencing3.17 Sequencing depth and coverage in bulk RNA sequencing3.18 Differential expression analysis in RNA sequencing3.19 Functional genomics and pathway analysis in RNA sequencing3.20 Emerging applications of bulk RNA sequencing in disease research, immunology, and oncology3.21 Challenges and limitations of current RNA sequencing methodologies3.22 Future directions and technologies in RNA sequencing3.23 Best practices for bulk RNA sequencing in the wet lab3.24 Ethical considerations in transcriptomics research3.25 ConclusionReferences4. Single-cell RNA sequencing in wet labAnton Buzdin, Xinmin Li, Maria Suntsova, and Ilya Belalov4.1 Overview of what scRNA-seq is and why it is indispensable in research4.2 Types of scRNA-seq protocols4.3 Reagents and materials4.4 scRNA-seq platforms: Comparison of chromium 10X, Drop-seq, and Smart-seq4.5 Sample preparation and handling4.6 Single-cell isolation techniques4.7 Library preparation4.8 Sequencing technologies4.9 Techniques to ensure the integrity and quality of scRNA-seq data4.10 Data analysis methods to validate the quality of sequencing results4.11 Recommended sequencing depths for different types of analyses4.12 Overview of computational tools and methods for analyzing scRNA-seq data4.13 Integrating scRNA-seq data with other data types4.14 Research and clinical applications of scRNA-seq4.15 Innovations and future trends in scRNA-seq technologyReferencesFurther reading5.