Next Generation Sequencing: Methods and Protocols

✍ Scribed by Steven R. Head,Phillip Ordoukhanian,Daniel R. Salomon (eds.)

• Publisher: Humana Press
• Year: 2018
• Tongue: English
• Leaves: 270
• Series: Methods in Molecular Biology 1712
• Edition: 1
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xiii
An Integrated Polysome Profiling and Ribosome Profiling Method to Investigate In Vivo Translatome (Hyun Yong Jin, Changchun Xiao)....Pages 1-18
Measuring Nascent Transcripts by Nascent-seq (Fei Xavier Chen, Stacy A. Marshall, Yu Deng, Sun Tianjiao)....Pages 19-26
Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis (Lieselot Deleye, Dieter De Coninck, Dieter Deforce, Filip Van Nieuwerburgh)....Pages 27-42
Multiplexed Targeted Sequencing for Oxford Nanopore MinION: A Detailed Library Preparation Procedure (Timokratis Karamitros, Gkikas Magiorkinis)....Pages 43-51
Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing (Bernard J. Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J. Park)....Pages 53-70
ClickSeq: Replacing Fragmentation and Enzymatic Ligation with Click-Chemistry to Prevent Sequence Chimeras (Elizabeth Jaworski, Andrew Routh)....Pages 71-85
Genome-Wide Analysis of DNA Methylation in Single Cells Using a Post-bisulfite Adapter Tagging Approach (Heather J. Lee, Sébastien A. Smallwood)....Pages 87-95
Sequencing of Genomes from Environmental Single Cells (Robert M. Bowers, Janey Lee, Tanja Woyke)....Pages 97-111
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, Marie Louis)....Pages 113-144
CleanTag Adapters Improve Small RNA Next-Generation Sequencing Library Preparation by Reducing Adapter Dimers (Sabrina Shore, Jordana M. Henderson, Anton P. McCaffrey)....Pages 145-161
Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities (Pedro J. Torres, Scott T. Kelley)....Pages 163-173
A Bloody Primer: Analysis of RNA-Seq from Tissue Admixtures (Casey P. Shannon, Chen Xi Yang, Scott J. Tebbutt)....Pages 175-201
Next-Generation Sequencing of Genome-Wide CRISPR Screens (Edwin H. Yau, Tariq M. Rana)....Pages 203-216
Gene Profiling and T Cell Receptor Sequencing from Antigen-Specific CD4 T Cells (Marie Holt, Anne Costanzo, Louis Gioia, Brian Abe, Andrew I. Su, Luc Teyton)....Pages 217-238
Investigate Global Chromosomal Interaction by Hi-C in Human Naive CD4 T Cells (Xiangzhi Meng, Nicole Riley, Ryan Thompson, Siddhartha Sharma)....Pages 239-252
Primer Extension, Capture, and On-Bead cDNA Ligation: An Efficient RNAseq Library Prep Method for Determining Reverse Transcription Termination Sites (Phillip Ordoukhanian, Jessica Nichols, Steven R. Head)....Pages 253-261
Back Matter ....Pages 263-266

✦ Subjects

Human Genetics