High Throughput Gene Screening Methods and Protocols

This volume explores the latest advancements in the high-throughput sequencing (HTS) technologies and its uses in our understanding of complex biological processes and human diseases. The chapters in this book are organized into five parts and cover topics such as genome based-sequencing technologies, including whole genome sequencing, targeted sequencing, and metagenomic analysis; epigenome-based technologies like EM-seq, MNase-seq, and ATAC-seq; transcriptome-based sequencing technologies, including RNA-seq, scRNA-seq, mi-RNA-seq and RIL-seq; HTS modalities for structural studies of DNA including Hi-C and DamID-seq; and the potential use of HTC in clinical settings, including cancer research and treatment, and personalized medicine. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, tips on troubleshooting, and avoiding known pitfalls.

Cutting-edge and thorough, High Throughput Gene Screening: Methods and Protocols is a valuable resource for all researchers interested in incorporating HTS into their research and learning more about this exciting technology.

The Evolution of Next-Generation Sequencing Technologies.- A Step-by-Step Guide to Sequencing and Assembly of Complete Bacterial Genomes using the Oxford Nanopore MinION.- Targeted Next-Generation Sequencing in Rare Diseases.- Collection and Processing of Samples for Next-Generation Sequencing to Study the Gut Microbiome.- Whole Genome Methylation Sequencing via Enzymatic Conversion (EM-seq): Protocol, Data Processing, and Analysis.- MNase-seq to Identify Genome-Wide DNA-Protein Interactions.- ATAC-seq for Characterizing Host and Pathogen Genome Accessibility during Virus Infection.- RNA Sequencing Protocols for Short-Read Sequencing.- Dissection of Gene Expression at the Single Cell Level: scRNA-seq.- The Study of Small RNA Sequencing from Biological Samples (miRNA-seq).- Biological Insights from RNA-RNA Interactomes in Bacteria, as Revealed by RIL-seq.- Extraction, Purification, and Next-Generation Sequencing (NGS) Analysis of DNA and RNA from Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue.- Using Chromosome Conformation Capture Combined with Deep Sequencing (Hi-C) to Study Genome Organization in Bacteria.- An Optimized Adaptation of DamID for NGS Applications.- How Have Massively Parallel Sequencing Technologies Furthered Our Understanding of Oncogenesis and Cancer Progression?.- The Use of Next-Generation Sequencing in Personalized Medicine.