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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.

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1. Overview of Gene Expression Analysis - Transcriptomics

Nalini Raghavachari and Natalia Reyero

2. RNA-Seq and Expression Arrays: Selection Guidelines for Genome-wide Expression Profiling

Jessica Minnier, Nathan D. Pennock , Quichen Guo, Pepper Schedin, and Christina A. Harrington

3. A Guide for Designing and Analysing RNA-Seq Data

Aniruddha Chatterjee, Antonio Ahn, Euan J Rodger, Peter A Stockwell, and Michael R Eccles

4. SureSelect XT RNA Direct: A Technique for Expression Analysis Through Sequencing of Target-enriched FFPE total RNA

Jennifer Carter Jones, Alex P. Siebold, Carolina Becker Livi, and Anne Bergstrom Lucas

5. Simultaneous, Multiplexed Detection of RNA and Protein on the NanoString © nCounter © Platform

Sarah Warren

6. Transcript Profiling Using Long-read Sequencing Technologies

Anthony Bayega, Yu Chang Wang, Spyros Oikonomopoulos, Haig Djambazian, Somayyeh Fahiminiya, and Jiannis Ragoussis

7. 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, and Stefan J. Green

8. microRNA Expression Analysis - Next Generation Sequencing

Poching Liu

9. Identification of Transcriptional Regulators that Bind to Long Noncoding RNAs by RNA Pull Down and RNA Immunoprecipitation

Xiangbo Ruan, Ping Li, and Haiming Cao

10. Single-cell mRNA-Seq using the Fluidigm C1 System and Integrated Fluidics Circuits

Haibiao Gong, Devin Do, and Ramesh Ramakrishnan

11. Current and Future Methods for mRNA Analysis: A Drive Towards Single Molecule Sequencing

Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, and Jiannis Ragoussis

12. Expression Profiling of Differentially Regulated Genes in Fanconi Anemia

Binita Zipporah E, Kavitha Govarthanan, Pavithra Shyamsunder, and Rama S Verma

13. A Review of Transcriptome Analysis in Pulmonary Vascular Diseases

Dustin R. Fraidenburg and Roberto F. Machado

14. Differential Gene Expression Analysis of Plants

Mark Arick II and Chuan-Yu Hsu

15. High Throughput Sequencing Based Approaches for Gene Expression Analysis.

R. Raja Sekhara Reddy and M. V. Ramanujam

16. Network Analysis of Gene Expression Roby Joehanes

17. Analysis of ChIP-Seq and RNA-Seq data with BioWardrobe

Sushmitha Vallabh, Andrey V. Kartashov, and Artem Barski

18. Bayesian Network to Infer Drug-induced Apoptosis Circuits from Connectivity Map Data

Jiyang Yu and Jose M. Silva

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