cDNA Libraries Methods and Applications

The numerous vital applications of complementary DNA (cDNA) technology have changed dramatically as the technology has advanced over recent years.  In cDNA Libraries: Methods and Protocols, expert researchers provide current techniques that reflect the latest advances in the construction and application of cDNA libraries.  The first half of the volume covers improved approaches to some of the most basic elements of creating cDNA libraries, while the second half casts a much wider net and includes visionary applications of cDNA technology which were either unforeseen or technically impractical until recently.  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 key tips on troubleshooting and avoiding known pitfalls.

Part I: Enhanced Approaches to Inherent Problems

1. Isolation of Fungal Infection Structures from Plant Tissue by Flow Cytometry for Cell-Specific Transcriptome Analysis

            Hiroyuki Takahara, Elmar Endl, and Richard O’Connell

2. Preparation of a High Quality cDNA Library from a Single-Cell Quantity of mRNA Using Chum-RNA

            Hiroshi Nojima and Takahiro Tougan

3. Construction of a Full-Length cDNA Library from Castor Endosperm for High-throughput Functional Screening

            Chaofu Lu, James G. Wallis, and John Browse

4. Full-Length Transcriptome Analysis Using a Bias-Free cDNA Library Prepared with the Vector-Capping Method

            Seishi Kato, Mio Oshikawa, and Kuniyo Ohtoko

5. Construction of Improved Yeast Two-Hybrid Libraries

            Richard H. Maier, Christina J. Maier, and Kamil Önder

6. Normalization of Full-Length Enriched cDNA

            Ekaterina A. Bogdanova, Ekaterina V. Barsova, Irina A. Shagina, Alexander Scheglov, Veronika Anisimova, Laura L. Vagner, Sergey A. Lukyanov, and Dmitry A. Shagin

7. Bioinformatic Methods for Finding Differentially Expressed Genes in cDNA Libraries, Applied to the Identification of Tumour Vascular Targets

            John M.J. Herbert, Dov J. Stekel, Manuela Mura, Michail Sychev, and Roy Bicknell

Part II: Visionary Applications

8. Enzymatic Production of RNAi Libraries from cDNAs and High-Throughput Selection of Effective shRNA Expression Constructs

            Kohtaroh Sugao and Kenzo Hirose

9. Construction of Small RNA cDNA Libraries for High-Throughput Sequencing

            Cheng Lu and Vikas Shedge

10. Focusing Mutations Within Random Libraries to Distinct Areas: Protein Domain Library Generation by Overlap Extension (PDLGO)

            Andreas Gratz and Joachim Jose

11. Generation of Families of Construct Variants Using Golden Gate Shuffling

            Carola Engler and Sylvestre Marillonnet

12. Application of Full-Length cDNA Resources to Gain-of-Function Technology for Characterization of Plant Gene Function

            Youichi Kondou, Mieko Higuchi, Takanari Ichikawa, and Minami Matsui

13. Construction of Yeast Surface-Displayed cDNA Libraries

            Scott Bidlingmaier and Bin Liu

14. Identification of Protein/Target Molecule Interactions Using Yeast Surface-Displayed cDNA Libraries

            Scott Bidlingmaier and Bin Liu

15. SNP Discovery by Transcriptome Pyrosequencing

            W. Brad Barbazuk and Patrick S. Schnable

16. RNA-seq Analysis of Gene Expression and Alternative Splicing by Double-Random Priming Strategy

            Michael T. Lovci, Hai-Ri Li, Xiang-dong Fu, and Gene W. Yeo

17. Generation of a Large Catalog of Unique Transcripts for Whole-Genome Expression Analysis in Non-Model Species

            Diana Bellin, Alberto Ferrarini, and Massimo Delledonne