Gene Expression Analysis

Description

This volume provides experimental and bioinformatics approaches related to different aspects of gene expression analysis. Divided in three sections chapters detail wet-lab protocols, bioinformatics approaches, single-cell gene expression, highly multiplexed amplicon sequencing, multi-omics techniques, and targeted sequencing. 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 cutting-edge, Gene Expression Analysis: Methods and Protocols aims provide useful information to researchers worldwide. Front Matter ....Pages i-xi Overview of Gene Expression Analysis: Transcriptomics (Nalini Raghavachari, Natàlia Garcia-Reyero)....Pages 1-6 RNA-Seq and Expression Arrays: Selection Guidelines for Genome-Wide Expression Profiling (Jessica Minnier, Nathan D. Pennock, Qiuchen Guo, Pepper Schedin, Christina A. Harrington)....Pages 7-33 A Guide for Designing and Analyzing RNA-Seq Data (Aniruddha Chatterjee, Antonio Ahn, Euan J. Rodger, Peter A. Stockwell, Michael R. Eccles)....Pages 35-80 SureSelectXT RNA Direct: A Technique for Expression Analysis Through Sequencing of Target-Enriched FFPE Total RNA (Jennifer Carter Jones, Alex P. Siebold, Carolina Becker Livi, Anne Bergstrom Lucas)....Pages 81-104 Simultaneous, Multiplexed Detection of RNA and Protein on the NanoString® nCounter® Platform (Sarah Warren)....Pages 105-120 Transcript Profiling Using Long-Read Sequencing Technologies (Anthony Bayega, Yu Chang Wang, Spyros Oikonomopoulos, Haig Djambazian, Somayyeh Fahiminiya, Jiannis Ragoussis)....Pages 121-147 Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol (Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J. Green)....Pages 149-169 MicroRNA Expression Analysis: Next-Generation Sequencing (Poching Liu)....Pages 171-183 Identification of Transcriptional Regulators That Bind to Long Noncoding RNAs by RNA Pull-Down and RNA Immunoprecipitation (Xiangbo Ruan, Ping Li, Haiming Cao)....Pages 185-191 Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits (Haibiao Gong, Devin Do, Ramesh Ramakrishnan)....Pages 193-207 Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing (Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, Jiannis Ragoussis)....Pages 209-241 Expression Profiling of Differentially Regulated Genes in Fanconi Anemia (Binita Zipporah E, Kavitha Govarthanan, Pavithra Shyamsunder, Rama S. Verma)....Pages 243-258 A Review of Transcriptome Analysis in Pulmonary Vascular Diseases (Dustin R. Fraidenburg, Roberto F. Machado)....Pages 259-277 Differential Gene Expression Analysis of Plants (Mark Arick II, Chuan-Yu Hsu)....Pages 279-298 High Throughput Sequencing-Based Approaches for Gene Expression Analysis (R. Raja Sekhara Reddy, M. V. Ramanujam)....Pages 299-323 Network Analysis of Gene Expression (Roby Joehanes)....Pages 325-341 Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe (Sushmitha Vallabh, Andrey V. Kartashov, Artem Barski)....Pages 343-360 Bayesian Network to Infer Drug-Induced Apoptosis Circuits from Connectivity Map Data (Jiyang Yu, Jose M. Silva)....Pages 361-378 Erratum to: RNA-Seq and Expression Arrays: Selection Guidelines for Genome-Wide Expression Profiling (Jessica Minnier, Nathan D. Pennock, Qiuchen Guo, Pepper Schedin, Christina A. Harrington)....Pages E1-E1 Back Matter ....Pages 379-387