Description
This volume covers a wide range of various fields of research, with the common thread being Next Generation Sequencing (NGS) related methods and applications, as well as analysis and interpretation of the data obtained. Chapters guide readers through the highly dynamic processes of translational and transcriptional profiling of a cell, method to detect copy number alterations (CNAs), targeted sequencing applications, method called “Hi-Plex” to characterize known polymorphic loci, single-cell of DNA or RNA, identify and characterize rare circulating CD4 T cells, and computational pipeline for RNAseq analysis. 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, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Next Generation Sequencing: Methods and Protocols aims to be useful and informative for further study into this vital field. 1. An Integrated Polysome Profiling and Ribosome Profiling Method to Investigate in vivo Translatome Hyun Yong Jin and Changchun Xiao 2. Measuring Nascent Transcripts by Nascent-seq Fei Xavier Chen, Stacy A. Marshall, and Yu Deng 3. Genome-wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis Lieselot Deleye, Dieter De Coninck, Dieter Deforce, and Filip Van Nieuwerburgh 4. Multiplexed Targeted Sequencing for Oxford Nanopore MinION; A Detailed Library Preparation Procedure Timokratis Karamitros and Gkikas Magiorkinis 5. Hi-Plex for Simple, Accurate, and Cost-effective Amplicon-based Targeted DNA Sequencing Bernard J Pope, Fleur Hammet, Tu Nguyen-Dumont, and Daniel J Park 6. ClickSeq: Replacing Fragmentation and Enzymatic Ligation with Click-Chemistry to Prevent Sequence Chimeras Elizabeth Jaworski and Andrew Routh 7. Genome-wide Analysis of DNA Methylation in Single Cells Using a Post-bisulfite Adapter Tagging Approach Heather J Lee and Sbastien A Smallwood 8. Sequencing of Genomes from Environmental Single Cells Robert M. Bowers, Janey Lee, and Tanja Woyke 9. SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms Phillip A. Morin, Andrew D. Foote, Christopher M. Hill, Benoit Simon-Bouhet, Aimee R. Lang, and Marie Louis 10. CleanTag Adapters Improve Small RNA Next-Generation Sequencing Library Preparation by Reducing Adapter Dimers Sabrina Shore, Jordana M. Henderson, and Anton P. McCaffrey 11. Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities Pedro J. Torres and Scott T. Kelley 12. A Bloody Primer Analysis of RNA-Seq from Tissue Admixtures Casey P. Shannon, Chen Xi Yang, and Scott J. Tebbutt 13. Next-Generation Sequencing of Genome-wide CRISPR Screens Edwin Yau and Tariq Rana 14. Gene Profiling and T Cell Receptor Sequencing from Antigen-specific CD4 T Cells Marie Holt, Anne Costanzo, Louis Gioia, Brian Abe, Andrew I. Su, and Luc Teyton 15. Investigate Global Chromosomal Interaction by Hi-C in Human Nave CD4 T Cells Xiangzhi Meng, Nicole Riley, Ryan Thompson, and Siddhartha Sharma 16. Primer Extension, Capture, and On-bead cDNA Ligation: An Efficient RNAseq Library Prep Method for Determining Reverse Transcription Termination Sites Phillip Ordoukhanian, Jessica Nichols, and Steven R Head
