Preface

RNA interference (RNAi), has developed into an important tool for gene function elucidation by leveraging this endogenous gene-silencing pathway with well-designed triggers for the systematic silencing of particular genes. Incorporation of RNAi into high throughput screening platforms has led to important discoveries in fields such as cancer biology and pathogenesis, successes driven by establishment of best-practices and developments in instrumentation, analysis, and the growing sophistication of cell-based assays. The following chapters represent some of the most important considerations and recent developments in RNAi screening technology. It is certainly our hope that this compendium contains something for everyone, both novice and experienced researchers alike.

The topics in this collection range from recent automation platforms for ultra-high throughput screens (see Chapters 2 and 8) to novel applications of this gene modulation technology to cells grown in 3D culture (see Chapter 9). Chapter 1 provides a review of RNAi as a research tool as well as experimental and bioinformatics approaches to reduce and identify off-target effects in highthroughput screening data. Important considerations regarding deposition of large data sets in public repositories are presented in Chapter 3. Pooled shRNA screening methods are discussed in Chapter 4. Chapters 5 and 6 describe how RNAi technologies are being used to interrogate the host-pathogen interface. RNAi screening in difficult-to-transfect immune cells is addressed in Chapter 7 and applications beyond target discovery are presented in Chapters 10 and 11.

While it is not evident at first glance, a research alliance underlies all the contributions detailed in this book. All authors are affiliated with a lab that participates in the RNAi Global Initiative, a world-wide association of biomedical researchers established to broaden and accelerate the utility and application of RNAi technology. Founded in 2005 with eleven member institutions, the organization focused on developing and disseminating information on the basics of RNAi screening. As the organization grew and technology developed, focus shifted toward more complex, often biological, challenges.

Nine years after its inauguration, the RNAi Global Initiative now includes over 60 academic institutes spread across five continents. Members continue to share their findings in a range of fields (stem cell biology, cancer, and host-pathogen interactions) and as evidenced by this book, collaborate in the development of new bioinfomatic tools, screening methods, and programs in applied biology. The longevity of this alliance is the result of continued contributions on the part of its membership and is a testament to the importance of collaboration in building a cohesive scientific community.