FISH : a practical approach

목차 (Table of Contents)

• CONTENTS
• List of protocols = xiii
• Abbreviations = xvii
• 1 Introduction / Sabine Mai ; Barbara G. Beatty ; Jeremy A. Squire = 1
• References = 4
• 2 FISH probes and labelling techniques / Patricia Bray-Ward = 5
• 1 Introduction = 5
• 2 Fluorescence principles = 5
• Fluors and haptens = 6
• Commonly used fluors = 7
• Choice of filter sets = 7
• 3 Nucleic probes = 8
• Types of probes = 8
• Preparation of cloned probes = 9
• Enzymatically amplified probes = 15
• Synthetic oligonucleotide probes = 16
• 4 Coupling of fluors／haptens to nucleotides = 17
• 5 Labelling of probes = 19
• Nick translation = 20
• Random primer labelling = 21
• RNA transcription labelling = 22
• PCR labelling = 24
• 6 Post-labelling DNA processing and purification = 25
• DNase treatment(for FISH and other hybridization protocols) = 25
• Removal of unincorporated nucleotides and BSA from the reaction mix prior to probe precipitation = 25
• 7 Other labelling systems = 26
• Coupling of fluors or haptens to amine-modified nucleic acids = 26
• Other chemical coupling systems = 26
• Direct chemical coupling of fluors or haptens to proteins = 26
• References = 27
• 3 Human chromosome mapping of single copy genes / Barbara G. Beatty ; Stephen W. Scherer = 29
• 1 Introduction = 29
• 2 DNA probes for FISH mapping = 30
• Identification of FISH probes from WWW sites = 30
• Preparation of probes for FISH mapping = 32
• 3 Target DNA preparation = 34
• Metaphase chromosomes = 34
• Mapping with interphase nuclei = 36
• Hypotonic treatment and fixation = 38
• 4 Slide preparation = 39
• Target slide pre-treatment = 41
• 5 Denaturation and hybridization of probe and target DNA = 42
• 6 Post-hybridization washes = 44
• 7 Immunodetection = 45
• 8 Chromosome counterstaining and banding = 47
• 9 Microscopy and image analysis = 48
• 10 FISH mapping points to consider = 49
• FISH mapping of single probes to metaphase chromosomes = 49
• Relational mapping with multiple probes = 51
• References = 53
• 4 Murine chromosome preparation / Sabine Mai ; Francis Wiener = 55
• 1 Murine chromosome preparation for banding and in situ hybridization procedures = 55
• Introduction = 55
• 2 Giemsa-trypsin banding of mouse chromosomes = 63
• 3 Molecular cytogenetic approaches for murine chromosomes = 66
• References = 76
• 5 High resolution FISH mapping using chromatin and DNA fibre / Henry H. Q. Heng = 77
• 1 Introduction = 77
• 2 Practical considerations for fibre preparation = 78
• 3 General equipment required for fibre FISH = 78
• 4 Chromatin fibre preparation = 79
• 5 DNA fibre preparation = 83
• 6 FISH = 85
• DNA probe labelling = 85
• Hybridization = 86
• Wash = 88
• Detection and amplification = 89
• Counterstaining and antifade = 90
• 7 Photography = 91
• Acknowledgements = 91
• References = 91
• 6 Applications of RNA FISH for visualizing gene expression and nuclear architecture / Rose Tam ; Lindsay S. Shopland ; Carol V. Johnson ; John A. McNeil ; Jeanne B. Lawrence = 93
• 1 Introduction = 93
• 2 Cell preparation = 96
• Detergent-extracted cell preparation = 96
• Cytogenetic preparations = 97
• 3 Probe preparation = 99
• 4 Hybridization to RNA = 100
• Basic RNA hybridization procedure = 101
• Oligonucleotide hybridization = 102
• 5 Hybridization to DNA = 103
• Detecting heat denautred cellular DNA = 104
• DNA FISH using NaOH denaturation and RNA hydrolysis = 105
• 6 Multiple label techniques and applications = 105
• Coupling the detection of RNA with DNA = 105
• Coupling protein detection with FISH = 107
• Chromosome paints and RNA FISH = 108
• Differentiating transcripts with intron and cDNA probes = 109
• Exon suppression hybridization : an example of the use of specific competition = 110
• 7 Visualizing and analysing results = 112
• Microscopy = 113
• Digital imaging = 114
• 8 Concluding remarks = 116
• Acknowledgements = 117
• References = 117
• 7 FISH on three-dimensionally preserved nuclei / I. Solovei ; J. Walter ; M. Cremer ; F. Habermann ; L. Schermelleh ; T. Cremer = 119
• 1 Introduction = 119
• 2 Preparation and fixation of cells = 123
• Preparation of slides = 123
• Cultivation and fixation of adherent cells = 125
• Preparation, attachment, and fixation of cells growing in suspension = 126
• 3 Preparation of cells directly isolated from peripheral blood = 127
• 4 Pre-treatments needed for hybridization = 128
• 5 Hybridization set-up = 131
• Probe labelling = 131
• Probe preparation = 132
• DNA denaturation and hybridization = 132
• 6 Post-hybridization washes, detection, nuclei counterstaining, and slide mounting = 134
• Post-hybridization washes = 134
• Detection of hybridized probes = 135
• Counterstaining of nuclei and mounting cells in antifade medium = 137
• 7 Combined 3D FISH and replication labelling = 139
• Replication labelling = 139
• Detection of incorporated halogenated deoxyuridines after FISH = 140
• 8 Combined protein immunodetection and 3D FISH = 142
• 9 Preservation of the chromatin structure during 3D FISH = 144
• 10 Confocal microscopy = 144
• Selection of the filter configuration = 147
• Conditions of image acquisition = 149
• Calibration of the instrument = 150
• Visualization = 150
• Quantitative measurements and deconvolution = 152
• References = 154
• 8 Comparative genomic hybridization of metaphase chromosomes and DNA chips / Stefan Joos ; Carsten Schw$$\ddot a$$nen ; Peter Lichter = 159
• 1 Introduction = 159
• 2 Preparation of metaphase chromosomes = 161
• 3 Isolation of genomic DNA = 161
• 4 Isolation of single cells by micromanipulation = 167
• 5 Amplification of genomic DNA from small cell populations by universal polymerase chain reaction(PCR) = 168
• 6 Probe labelling = 172
• 7 Comparative genomic hybridization = 174
• Denaturation of metaphase chromosomes = 174
• Probe mixture = 175
• In situ hybridization and signal detection = 176
• 8 Image acquisition and evaluation = 177
• 9 Troubleshooting of CGH experiments = 178
• 10 Troubleshooting of CGH experiments in combination with universal PCR = 179
• 11 New developments : matrix-CGH = 180
• References = 181
• 9 FISH in clinical cytogenetics / Jeremy A. Squire ; P. Marrano ; E. Kolomietz = 183
• 1 Introduction = 183
• 2 Probes commonly used for FISH in the clinical laboratory = 184
• 3 Preparation of clinical samples for FISH analysis = 185
• Preparation of metaphase chromosomes for FISH = 185
• Preparation of interphase nuclei derived from clinical specimens for FISH = 187
• 4 Criteria for assessing and reporting FISH results = 194
• General considerations when selecting cells for FISH microscopy = 195
• Scoring criteria for interphase FISH signal evaluation and enumeration = 196
• Special considerations concerning interphase FISH interpretation = 197
• 5 Some of the commonly used FISH probes in clinical cytogenetics = 198
• FISH analysis of microdeletion syndromes = 198
• Use of the three-colour fusion(translocation／inversion) probes = 199
• Use of FISH probes in assessing gene amplification = 201
• 6 Appendix(useful web sites for molecular cytogenetics clinical sources) = 202
• References = 202
• 10 Multicolour FISH and spectral karyotyping / Jane Bayani ; Jeremy A. Squire = 205
• 1 Introduction = 205
• 2 Spectral karyotyping(SKY) = 206
• 3 M-FISH = 208
• 4 M-FISH and SKY protocols = 208
• 5 General considerations for image acquisition and analysis = 214
• Image analysis using SKY = 215
• Image analysis using M-FISH = 216
• 6 Troubleshooting = 216
• References = 219
• 11 cDNA microarrays for fluorescent hybridization analysis of gene expression / Javed Khan ; Lao H. Saal ; Michael L. Bittner ; Yuan Jiang ; Gerald C. Gooden ; Arthur A. Glatfelter ; Paul S. Meltzer = 221
• 1 Introduction = 221
• Serial analysis of gene expression = 221
• Oligonucleotide arrays = 222
• cDNA microarrays = 222
• 2 Fabrication of cDNA microarrays = 223
• Culturing cDNA bacterial clones = 223
• Microarray slide printing = 230
• 3 Target production = 232
• 4 Hybridization = 235
• 5 Image acquisition = 237
• 6 Image analysis and normalization = 237
• 7 Sensitivity and specificity = 238
• 8 Data mining and statistical analysis = 238
• 9 Summary = 239
• References = 239
• List of suppliers = 241
• Index = 251