Microarrays: Volume 2, Applications and Data Analysis

ISBN-13: 9781617378522 / Angielski / Miękka / 2010 / 452 str.

Jang B. Rampal

Opis

Microarray Technology, Volumes 1 and 2, present information in designing and fabricating arrays and binding studies with biological analytes while providing the reader with a broad description of microarray technology tools and their potential applications. The first volume deals with methods and protocols for the preparation of microarrays. The second volume details applications and data analysis, which is important in analyzing the enormous data coming out of microarray experiments. Among the topics discussed in Volume 1: Synthesis Methods, are matrices in the synthesis of microarrays, array optimization processes, array-based comparative genomic hybridization, 60-mer oligonucleotide probes, bifunctional reagents NTMTA and NTPAC, and high density arrays using digital microarray synthesis platforms. Other topics include multiplex ligation-dependent probe amplification (MLPA), hybridization conditions in situ-synthesized oligo arrays, peptide arrays, high density replication tools (HDRT), protocols for the quantification of oligo hybridization, glyco-bead arrays, and an investigation into the emerging nano technology. Volume 2: Applications and Data Analysis includes insight into non-mammalian vertebrate systems, processes and protocols for high quality glass-based microarrays. Applications in DNA, peptide, antibody and carbohydrate microarraying, oligonucleotide microarrays generated from hydrolysis PCR probe sequences, microarray platforms in clinical practice, and screening of cDNA libraries on glass slide microarrays. Authors in this volume also discuss paraflo biochip for nucleic acid and protein analysis, volumetric mass spectrometry protein arrays, protocols for predicting DNA duplex stability on oligonucleotide arrays, and integrated analysis of microarray results. Microarray Technology, Volumes 1 and 2, provide ample information to all levels of scientists from novice to those intimately familiar with array technology.

Spis treści

Table of Contents Microarray Technology Volume 2 - Applications and Data Analysis 1. The Use of Microarray Technology in Non-mammalian Vertebrate Systems Conor W. Sipe and Margaret S. Saha 2. Quality Considerations and Selection of Surface Chemistry for Glass-Based DNA, Peptide, Antibody, Carbohydrate, and Small Molecule Microarrays. Jens Sobek*, Catharine Aquino and Ralph Schlapbach 3. Optimization Workflow for the Processing of High Quality Glass-Based Microarrays. Application in DNA, Peptide, Antibody, and Carbohydrate Microarraying. Jens Sobek*, Catharine Aquino and Ralph Schlapbach 4. Processing Protocols for High Quality Glass-Based Microarrays. Application in DNA, Peptide, Antibody and Carbohydrate Microarraying. Jens Sobek*, Catharine Aquino and Ralph Schlapbach 5. Specific Detection of Bacterial Pathogens Using Oligonucleotide Microarrays Generated from Hydrolysis PCR Probe Sequences Philip J.R.Day 6. Uses of Microarray Platforms in Cancer: A Correlative Study between Genomic Copy Number Changes and Their Expression at mRNA and Protein Level Fahd Al-Mulla 7. Microarray Technology for Use in Molecular Epidemiology Suzanne D. Vernon and Toni Whistler 8. Utilization of Microarray Platforms in Clinical Practice: An Insight on the Preparation and Amplification of Nucleic Acids from Frozen and Fixed Tissues Fahd Al-Mulla 9. A Microarray Based Method to Profile Global microRNA Expression in Human and Mouse Ranjan Perera 10. Genotyping of Single Nucleotide Polymorphisms by Arrayed Primer Extension Scott J. Tebbutt 11. Protein Chip for Detection of DNA Mutations Xian-En Zhang and Li-Jun Bi 12. Screening of cDNA Libraries on Glass Slide Microarrays. Dave K Berger, Bridget G. Crampton, Ingo Hein and Wiesner Vos 13. Automated Target Preparation Methods for Affymetrix Gene Expression Cartridges Handy Yowanto 14. Tumor-Stroma Interactions of Metastatic Prostate Cancer Cells Lines - Analysis Using Microarrays Nicolas Wernert, Annette Kaminski, El-Mustapha Haddouti and Jens Claus Hahne 15. Identification of Small Molecule Targets on Functional Protein Microarrays Michael Salcius, Gregory A. Michaud, Berry Schweitzer and Paul F. Predki 16. Quantification of Small Molecules Using Microarray Technology Martin Dufva and Claus BV Christensen 17. Antibody-microarrays on Hybrid Polymeric Thin Film Coated Slides for Multiple-protein Immunoassays Xichun Zhou and Jizhong Zhou 18. Overprint Immunoassay Using Protein A Microarrays Robert S. Matson, Raymond C. Milton, Jang B. Rampal, Tom S. Chan, and Michael C. Cress 19. ºParaflo Biochip for Nucleic Acid and Protein Analysis Qi Zhu, Ailing Hong, Nijing Sheng, Xiaolin Zhang, Anna Matejko, Kyu-Yeon Jun, Onnop Srivannavit, Erdogan Gulari, Xiaolian Gao and Xiaochuan Zhou 20. Application of Protein Chip Array Profiling in Serum Biomarker Discovery for Patients Suffering from Severe Acute Respiratory Syndrome (SARS) Timothy T. C. Yip, William C. S. Cho, Wai-Wai Cheng, Johnny W. M. Chan, Victor W. S. Ma, Tai-Tung Yip,Christine Yip, Roger K. C. Ngan and Stephen C. K. Law 21. Volumetric Mass Spectrometry Protein Arrays Dobrin Nedelkov, Urban A. Kiernan, Eric E. Niederkofler, Kemmons A. Tubbs and Randall W. Nelson 22. Microarray Data Classified by Artificial Neural Networks Roland Linder, Tereza Richards, Mathias Wagner 23. Methods for Microarray Data Analysis Veronique De Bruyne, Fahd Al-Mulla, Bruno Pot 24. Predicting DNA Duplex Stability on Oligonucleotide Arrays Arnold Vainrub, Norha Deluge, Xiaolin Zhang, Xiaochuan Zhou, and Xiaolian