| List of protocols |
| Abbreviations |
| Introduction / Sabine Mai ; Barbara G. Beatty ; Jeremy A. Squire1： |
| References |
| FISH probes and labelling techniques / Patricia Bray-Ward2： |
| Fluorescence principles |
| Fluors and haptens |
| Commonly used fluors |
| Choice of filter sets |
| Nucleic acid probes / 3： |
| Types of probes |
| Preparation of cloned probes |
| Enzymatically amplified probes |
| Synthetic oligonucleotide probes |
| Coupling of fluors/haptens to nucleotides / 4： |
| Labelling of probes / 5： |
| Nick translation |
| Random primer labelling |
| RNA transcription labelling |
| PCR labelling |
| Post-labelling DNA processing and purification / 6： |
| DNase treatment (for FISH and other hybridization protocols) |
| Removal of unincorporated nucleotides and BSA from the reaction mix prior to probe precipitation |
| Other labelling systems / 7： |
| Coupling of fluors or haptens to amine-modified nucleic acids |
| Other chemical coupling systems |
| Direct chemical coupling of fluors or haptens to proteins |
| Human chromosome mapping of single copy genes / Stephen W. Scherer |
| DNA probes for FISH mapping |
| Identification of FISH probes from WWW sites |
| Preparation of probes for FISH mapping |
| Target DNA preparation |
| Metaphase chromosomes |
| Mapping with interphase nuclei |
| Hypotonic treatment and fixation |
| Slide preparation |
| Target slide pre-treatment |
| Denaturation and hybridization of probe and target DNA |
| Post-hybridization washes |
| Immunodetection |
| Chromosome counterstaining and banding / 8： |
| Microscopy and image analysis / 9： |
| FISH mapping points to consider / 10： |
| FISH mapping of single probes to metaphase chromosomes |
| Relational mapping with multiple probes |
| Murine chromosome preparation / Francis Wiener |
| Murine chromosome preparation for banding and in situ hybridization procedures |
| Giemsa-trypsin banding of mouse chromosomes |
| Molecular cytogenetic approaches for murine chromosomes |
| High resolution FISH mapping using chromatin and DNA fibre / Henry H. Q. Heng |
| Practical considerations for fibre preparation |
| General equipment required for fibre FISH |
| Chromatin fibre preparation |
| DNA fibre preparation |
| FISH |
| DNA probe labelling |
| Hybridization |
| Wash |
| Detection and amplification |
| Counterstaining and antifade |
| Photography |
| Acknowledgements |
| 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 |
| Cell preparation |
| Detergent-extracted cell preparation |
| Cytogenetic preparations |
| Probe preparation |
| Hybridization to RNA |
| Basic RNA hybridization procedure |
| Oligonucleotide hybridization |
| Hybridization to DNA |
| Detecting heat denatured cellular DNA |
| DNA FISH using NaOH denaturation and RNA hydrolysis |
| Multiple label techniques and applications |
| Coupling the detection of RNA with DNA |
| Coupling protein detection with FISH |
| Chromosome paints and RNA FISH |
| Differentiating transcripts with intron and cDNA probes |
| Exon suppression hybridization: an example of the use of specific competition |
| Visualizing and analysing results |
| Microscopy |
| Digital imaging |
| Concluding remarks |
| FISH on three-dimensionally preserved nuclei / I. Solovei ; J. Walter ; M. Cremer ; F. Habermann ; L. Schermelleh ; T. Cremer |
| Preparation and fixation of cells |
| Preparation of slides |
| Cultivation and fixation of adherent cells |
| Preparation, attachment, and fixation of cells growing in suspension |
| Preparation of cells directly isolated from peripheral blood |
| Pre-treatments needed for hybridization |
| Hybridization set-up |
| Probe labelling |
| DNA denaturation and hybridization |
| Post-hybridization washes, detection, nuclei counterstaining, and slide mounting |
| Detection of hybridized probes |
| Counterstaining of nuclei and mounting cells in antifade medium |
| Combined 3D FISH and replication labelling |
| Replication labelling |
| Detection of incorporated halogenated deoxyuridines after FISH |
| Combined protein immunodetection and 3D FISH |
| Preservation of the chromatin structure during 3D FISH |
| Confocal microscopy |
| Selection of the filter configuration |
| Conditions of image acquisition |
| Calibration of the instrument |
| Visualization |
| Quantitative measurements and deconvolution |
| Comparative genomic hybridization on metaphase chromosomes and DNA chips / Stefan Joos ; Carsten Schwanen ; Peter Lichter |
| Preparation of metaphase chromosomes |
| Isolation of genomic DNA |
| Isolation of single cells by micromanipulation |
| Amplification of genomic DNA from small cell populations by universal polymerase chain reaction (PCR) |
| Comparative genomic hybridization |
| Denaturation of metaphase chromosomes |
| Probe mixture |
| In situ hybridization and signal detection |
| Image acquisition and evaluation |
| Troubleshooting of CGH experiments |
| Troubleshooting of CGH experiments in combination with universal PCR |
| New developments: matrix-CGH / 11： |
| FISH in clinical cytogenetics / P. Marrano ; E. Kolomietz |
| Probes commonly used for FISH in the clinical laboratory |
| Preparation of clinical samples for FISH analysis |
| Preparation of metaphase chromosomes for FISH |
| Preparation of interphase nuclei derived from clinical specimens for FISH |
| Criteria for assessing and reporting FISH results |
| General considerations when selecting cells for FISH microscopy |
| Scoring criteria for interphase FISH signal evaluation and enumeration |
| Special considerations concerning interphase FISH interpretation |
| Some of the commonly used FISH probes in clinical cytogenetics |
| FISH analysis of microdeletion syndromes |
| Use of the three-colour fusion (translocation/inversion) probes |
| Use of FISH probes in assessing gene amplification |
| Appendix (useful web sites for molecular cytogenetics clinical sources) |
| Multicolour FISH and spectral karyotyping / Jane Bayani |
| Spectral karyotyping (SKY) |
| M-FISH |
| M-FISH and SKY protocols |
| General considerations for image acquisition and analysis |
| Image analysis using SKY |
| Image analysis using M-FISH |
| Troubleshooting |
| 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 |
| Serial analysis of gene expression |
| Oligonucleotide arrays |
| cDNA microarrays |
| Fabrication of cDNA microarrays |
| Culturing cDNA bacterial clones |
| Microarray slide printing |
| Target production |
| Image acquisition |
| Image analysis and normalization |
| Sensitivity and specificity |
| Data mining and statistical analysis |
| Summary |
| List of suppliers |
| Index |
| List of protocols |
| Abbreviations |
| Introduction / Sabine Mai ; Barbara G. Beatty ; Jeremy A. Squire1： |
| References |
| FISH probes and labelling techniques / Patricia Bray-Ward2： |
| Fluorescence principles |
