UID:
almafu_9958128897102883
Format:
1 online resource (961 p.)
Edition:
2nd ed.
ISBN:
9786612755590
,
9786613837462
,
9781282755598
,
1282755595
,
9781283525015
,
1283525011
,
9780080575131
,
0080575137
,
9780123751737
,
012375173X
Series Statement:
Methods in enzymology, v. 470
Content:
This fully updated edition of the best-selling three-part Methods in Enzymology series, Guide to Yeast Genetics and Molecular Cell Biology is specifically designed to meet the needs of graduate students, postdoctoral students, and researchers by providing all the up-to-date methods necessary to study genes in yeast. Procedures are included that enable newcomers to set up a yeast laboratory and to master basic manipulations. This volume serves as an essential reference for any beginning or experienced researcher in the field. Provides up-to-date methods necessary to
Note:
Includes index.
,
Front Cover; Methods in Enzymology; Copyright Page; Contents; Contributors; Preface; Volumes in Series; Section 1: Functional Genomics; Chapter 1: Analysis of Gene Function Using DNA Microarrays; 1. Introduction and Experimental Design; 1.1. Single-mutant analysis; 1.2. Double-mutant analysis; 2. Methods; 2.1. Experimental design; 2.2. Cell growth; 2.3. Total RNA isolation and purification; 2.4. Purification of poly-A RNA; 2.5. Reverse transcription and dye labeling; 2.6. Hybridization; 2.7. Microarray washing; 2.8. Array scanning; 2.9. Gridding and normalization; References
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Chapter 2: An Introduction to Microarray Data Analysis and Visualization1. Introduction; 1.1. Overview; 1.2. Commonly used terms in microarray data analysis; 1.3. A simple case study; 2. Experimental Design: Single-Sample Versus Competitive Hybridization; 2.1. Single-sample hybridization; 2.2. Competitive hybridization; 2.3. Choosing the best approach; 3. Image Analysis; 3.1. What is a digital image?; 3.2. Data files; 3.3. Software tools; 4. Preprocessing; 4.1. Software tools; 4.2. Calculating ratio values; 4.3. Normalizing ratio values
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4.4. Quality assessment, filtering, and handling replicates4.5. Preprocessing Affymetrix arrays; 5. Visualizing Data Using Cluster Analysis; 5.1. Hierarchical clustering; 5.2. Partitioning and network-based approaches; 6. Assessing the Statistical Evidence for Differential Expression; 6.1. Significance analysis of microarrays; 6.2. Limma; 7. Exploring Gene Sets; 7.1. Gene Ontology term mapping; 7.2. Motif searching; 7.3. Network visualization; 7.4. Graphing array data on genome tracks; 8. Managing Data; 8.1. Data persistence and integrity; 8.2. Public data repositories and MIAME compliance
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AcknowledgmentsReferences; Chapter 3: Genome-Wide Approaches to Monitor Pre-mRNA Splicing; 1. Introduction; 2. Microarray Design; 3. Sample Preparation; 3.1. Cell collection; 3.2. RNA isolation; 3.3. cDNA synthesis; 3.4. Fluorescent labeling of cDNA; 3.5. Microarray hybridization; 3.6. Microarray washing; 4. Microarray Data Collection; 5. Microarray Data Analysis; 5.1. Data normalization; 5.2. Replication; 5.3. Splicing specific data; 5.4. Extracting biological meaning; 6. Future Methodologies; Acknowledgments; References
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Chapter 4: ChIP-Seq: Using High-Throughput DNA Sequencing for Genome-Wide Identification of Transcription Factor Binding Site1. Introduction; 2. Protocols; 2.1. Chromatin immunoprecipitation; 2.2. Input DNA preparation; 2.3. Illumina sequencing DNA library generation; 2.4. Barcode design and adapter annealing; 2.5. Illumina sequencing; 3. Sequencing Data Management; 4. Genome Analysis Pipeline; 5. Examining Data Quality and Parsing Barcoded Data; 6. Visualization in Genome Browser; 6.1. Low-level analysis; 6.2. High-level analysis; 6.3. Troubleshooting; 7. Conclusion and Future Directions
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Acknowledgments
Additional Edition:
ISBN 9780123751720
Additional Edition:
ISBN 0123751721
Language:
English
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