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E-raamat: DNA Microarrays

Edited by (Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Sweden)
  • Formaat: 299 pages
  • Sari: Advanced Methods
  • Ilmumisaeg: 24-Jan-2007
  • Kirjastus: Taylor & Francis Ltd
  • Keel: eng
  • ISBN-13: 9781134243990
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DNA MicroarraysSuurem pilt
  • Formaat: 299 pages
  • Sari: Advanced Methods
  • Ilmumisaeg: 24-Jan-2007
  • Kirjastus: Taylor & Francis Ltd
  • Keel: eng
  • ISBN-13: 9781134243990
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For advanced undergraduates, graduate students, and research scientists, Nuber (human molecular genetics, Max Planck Institute for Molecular Genetics, Germany) compiles 22 chapters that discuss DNA microarrays made up of immobilized DNA molecules, and their applications in toxicology, gene expression profiling, the diagnosis of cancer, eye diseases, stem cell research, genotyping, profiling, chromosome analysis, scanning, data analysis, clustering and classification, and image acquisition. Annotation ©2006 Book News, Inc., Portland, OR (booknews.com)
Abbreviations xi
Introduction: DNA Microarrays -- Ten Years Old, but no Old Hat
1(6)
Falk Hertwig
Ulrike A Nuber
How to perform a microarray experiment
3(4)
cDNA Microarray Analysis and its Role in Toxicology -- a Case Study
7(18)
Alexandra N Heinloth
Gary A Boorman
Richard S Paules
Introduction
7(3)
Gene expression profiling reveals indicators of potential adverse effects
10(3)
cDNA microarrays -- curse or blessing?
13(1)
The future ot toxicogenomics -- prediction of toxicity
13(12)
Protocol 2.1: In-life study
17(2)
Protocol 2.2: Gene expression analysis
19(2)
Protocol 2.3: Clinical pathology
21(1)
Protocol 2.4: Histopathology
22(1)
Protocol 2.5: Electron microscopy
23(1)
Protocol 2.6: ATP measurements
24(1)
Gene Expression Profiling in Plants Using cDNA Microarrays
25(14)
Motoaki Seki
Junko Ishida
Maiko Nakajima
Akiko Enju
Ayako Kamei
Youko Oono
Mari Narusaka
Masakazu Satou
Tetsuya Sakurai
Kazuo Shinozaki
Introduction
25(1)
Gene expression profiling methods
25(2)
DNA microarrays: cDNA and oligonucleotide microarrays
27(1)
cDNA clones and their application for cDNA microarray analysis
27(12)
Protocol 3.1: Preparation of cDNA microarrays
32(2)
Protocol 3.2: Preparation of cDNA targets
34(3)
Protocol 3.3: Microarray hybridization and scanning
37(1)
Protocol 3.4: Data analysis
38(1)
Identification of Gene Expression Patterns for a Molecular Diagnosis of Kidney Tumors
39(12)
Holger Sultmann
Andreas Buneß
Markus Ruschhaupt
Wolfgang Huber
Ruprecht Kuner
Bastian Gunawan
Laszlo Fuzesi
Annemarie Poustka
Introduction
39(1)
Experimental design
40(1)
Molecular classification of kidney tumors
40(1)
Building a classifier for kidney tumor diagnosis
41(1)
Summary
42(9)
Protocol 4.1: Tissue samples and RNA isolation
46(1)
Protocol 4.2: Microarray experiments
47(1)
Protocol 4.3: RNA labeling and hybridization
48(1)
Protocol 4.4: Signal quantification and data analysis
49(2)
Gene Expression Analysis of Differentiating Neural Progenitor Cells -- a Time Course Study
51(14)
Ulf Gurok
Ulrike A Nuber
Introduction
51(1)
The experiment
51(2)
Summary
53(12)
Protocol 5.1: Microarray production
56(2)
Protocol 5.2: Cell culture and RNA preparation
58(1)
Protocol 5.3: Hybridization, washing and scanning
59(3)
Protocol 5.4: Data processing
62(1)
Protocol 5.5: Cluster analysis
63(2)
A Microarray-Based Screening Method for Known and Novel SNPs
65(18)
Ena Wang
Francesco M Marincola
Introduction
65(1)
High resolution SNP detection methods
66(1)
High throughput methods for SNP detection
66(1)
Screening methods for known and unknown SNPs
67(3)
Summary
70(13)
Protocol 6.1: Target preparation
76(7)
From Gene Chips to Disease Chips -- New Approach in Molecular Diagnosis of Eye Diseases
83(14)
Rando Allikmets
Jana Zernant
Introduction
83(1)
APEX -- arrayed primer extension
84(1)
Application A -- the gene array for ABCA4-associated retinal dystrophies
85(3)
Application B -- the `disease array' for a genetically heterogeneous disorder (LCA)
88(2)
Summary
90(7)
Protocol 7.1: Template preparation
95(2)
Multiplexed SNP Genotyping Using Allele-Specific Primer Extension on Microarrays
97(14)
Juha Saharinen
Pekka Ellonen
Janna Saarela
Leena Peltonen
Introduction
97(2)
Practical approach on microarray-based allele-specific primer extension
99(6)
Data analysis -- allele calling and genotype assignment
105(2)
Summary
107(4)
Profiling the Arabidopsis Transcriptome
111(14)
Lars Hennig
Introduction
111(1)
MIAME/Plant -- documentation of the experiment
112(1)
RNA extraction
112(1)
Labeling
112(1)
Hybridization
112(1)
Washing, staining and scanning
113(1)
Data pre-processing and data analysis
113(1)
Useful tips
113(1)
Summary
114(11)
Protocol 9.1: RNA extraction
118(1)
Protocol 9.2: Labeling
119(2)
Protocol 9.3: Hybridization
121(2)
Protocol 9.4: Washing, staining and scanning
123(2)
Affymetrix GeneChip Analyses -- the Impact of RNA Quality
125(14)
Ludger Klein-Hitpass
Tarik Moroy
Introduction
125(3)
Aim and experimental design
128(1)
Statistics of RNA and array quality parameters
128(1)
Comparison of signal measures computed by different array normalization procedures in control and degraded samples
129(2)
SAM of degraded versus control RNA
131(1)
Summary
132(7)
Protocol 10.1: Affymetrix GeneChip analyses
137(2)
Molecular Karyotyping by Means of Array CGH: Linking Gene Dosage Alterations to Disease Phenotypes
139(18)
Joris Veltman
Lisenka Vissers
Introduction
139(1)
Array preparation, labeling, hybridization and data analysis
140(1)
Molecular karyotyping in clinical genetics
141(2)
Gene identification by array CGH
143(1)
Summary
144(13)
Protocol 11.1: Clone preparation and array fabrication
150(2)
Protocol 11.2: Array CGH procedure
152(3)
Protocol 11.3: Hybridization and posthybridization procedure
155(2)
DNA Microarrays: Analysis of Chromosomes and Their Aberrations
157(14)
Heike Fiegler
Susan M Gribble
Nigel Carter
Introduction
157(1)
Array construction and application of genomic microarrays
157(5)
Conclusion
162(9)
Protocol 12.1: DOP PCR
165(1)
Protocol 12.2: Aminolinking PCR
166(1)
Protocol 12.3: DOP PCR amplification of flow-sorted chromosomes
167(1)
Protocol 12.4: Random primed labeling of DNA for array CGH
168(1)
Protocol 12.5: Array hybridization
169(2)
Mapping Transcription Factor Binding Sites Using ChIP-Chip -- General Considerations
171(8)
Rebecca Martone
Micheal Snyder
Introduction
171(1)
Experimental approach
172(1)
Experimental considerations
173(1)
Data analysis
173(1)
Array selection
174(3)
Conclusion
177(2)
ChIP-on-Chip: Searching For Novel Transcription Factor Targets
179(12)
Esteban Ballestar
Manel Esteller
Introduction
179(1)
Genomic microarrays
180(1)
Performing a successful ChIP assay
181(2)
Obtaining material for hybridization
183(1)
Labeling and hybridizing the DNA
183(1)
Validating ChIP-on-chip results
184(1)
Summary
184(7)
Protocol 14.1: Performing a successful ChIP assay
188(3)
Turning Photons into Results: Principles of Fluorescent Microarray Scanning
191(12)
Siobhan Picket
Damian Verdnik
Introduction
191(1)
Scanning parameters
191(5)
Analysis parameters
196(3)
Normalization
199(4)
Microarray Detection with Laser Scanning Device
203(12)
Ralph Beneke
Introduction
203(1)
CCD or PMT?
203(2)
Engineering of Tecan's LS series
205(10)
Normalization Strategies for Microarray Data Analysis
215(12)
Christine Steinhoff
Martin Vingron
Introduction
215(2)
Experimental data
217(1)
Normalization methods
217(1)
Scaling methods
218(1)
Transformation methods
219(2)
Application of normalization methods
221(2)
Summary
223(4)
Microarray Data Analysis: Differential Gene Expression
227(14)
Stefanie Scheid
Rainer Spang
Introduction
227(1)
Getting started
227(3)
Explorative analysis
230(5)
Statistical analysis
235(3)
Final remarks
238(3)
Clustering and Classification Methods for Gene Expression Data Analysis
241(16)
Elizabeth Garrett-Mayer
Giovanni Parmigiani
Introduction
241(1)
Clustering
242(6)
Classification
248(4)
Summary
252(5)
Statistical Analysis of Microarray Time Course Data
257(24)
Yu Chaun Tai
Terence P Speed
Introduction
257(3)
Design
260(2)
Identifying the genes of interest
262(10)
Clustering
272(1)
Curve alignment
273(1)
Software
273(1)
Remarks
274(7)
Array CGH Data Analysis
281(10)
Yuedong Wang
Sun-Wei Guo
Introduction
281(1)
Summary
282(4)
Concluding remarks
286(5)
MIAME
291(6)
Robert Wagner
Introduction
291(1)
The structure of MIAME
291(1)
Array design description
292(1)
Experiment description
293(4)
Index 297


Ulrike Nuber-Max Planck Institute of Molecular Genetics, Berlin, Germany
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