List of Contributors |
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xv | (2) |
Abbreviations |
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xvii | |
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1. Fixation of tissues for the polymerase chain reaction |
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1 | (10) |
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1 | (1) |
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2. Reaction of fixatives with nucleic acids |
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2 | (1) |
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3 | (5) |
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3 | (1) |
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4 | (1) |
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5 | (1) |
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6 | (1) |
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Concentration of fixatives |
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6 | (1) |
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6 | (1) |
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Hydrogen ion concentration and buffers |
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6 | (1) |
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Microwave fixation/stabilization |
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7 | (1) |
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8 | (1) |
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9 | (1) |
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9 | (2) |
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2. In situ genetic analysis with selective ultraviolet radiation fractionation (SURF) |
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11 | (16) |
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11 | (2) |
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11 | (1) |
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12 | (1) |
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13 | (10) |
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Suitable tissues and PCR targets |
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13 | (1) |
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13 | (3) |
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Dotting of selected cells |
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16 | (3) |
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19 | (2) |
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21 | (1) |
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22 | (1) |
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Data presentation and analysis |
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22 | (1) |
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23 | (3) |
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Tumour evolution: out-of-Africa, out-of-adenoma |
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25 | (1) |
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26 | (1) |
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26 | (1) |
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27 | (26) |
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27 | (1) |
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28 | (1) |
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29 | (1) |
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30 | (1) |
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30 | (1) |
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30 | (1) |
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30 | (1) |
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Probe labelling check using nylon membranes |
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30 | (1) |
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31 | (3) |
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6. Specimen collection and fixation |
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34 | (1) |
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7. Preparation of RNase/DNase-free solutions, glassware, and plastics |
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34 | (1) |
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35 | (1) |
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36 | (1) |
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36 | (2) |
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36 | (1) |
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Blocking of non-specific probe interactions |
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37 | (1) |
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38 | (1) |
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12. Hybridization parameters |
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38 | (2) |
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38 | (1) |
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39 | (1) |
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39 | (1) |
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40 | (1) |
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13. Post-hybridization washes |
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40 | (1) |
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41 | (5) |
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46 | (4) |
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50 | (1) |
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50 | (3) |
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4. PCR in situ hybridization (PCR ISH) |
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53 | (34) |
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53 | (1) |
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2. Definitions and terminology |
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53 | (1) |
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3. Principles of the techniques |
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54 | (1) |
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4. Materials and equipment |
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54 | (1) |
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5. Tissue fixation and preparation |
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55 | (1) |
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55 | (1) |
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55 | (1) |
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Exposure of nucleic acid template |
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55 | (1) |
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6. Amplification: reagents and conditions |
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56 | (1) |
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7. Post-amplification washing and fixation |
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56 | (1) |
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8. Visualization of PCR product |
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57 | (1) |
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9. Reaction, tissue, and detection controls |
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57 | (1) |
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10. Problems associated with the techniques |
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58 | (1) |
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Sequestration of reagents |
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59 | (1) |
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59 | (1) |
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59 | (1) |
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59 | (1) |
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60 | (25) |
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Preparation of slides, cells, and tissue specimens |
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60 | (2) |
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Tissue and cell pre-treatment |
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62 | (3) |
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65 | (4) |
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69 | (8) |
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Post-hybridization washing |
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77 | (1) |
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Detection of hybridization signal |
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78 | (7) |
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85 | (2) |
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5. Reverse transcriptase in situ PCR for RNA detection |
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87 | (16) |
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87 | (1) |
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2. Preparation of cells for RT-PCR |
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88 | (2) |
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3. Reverse transcriptase reaction (first-strand cDNA synthesis) |
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90 | (2) |
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4. PCR with fluorescent primers |
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92 | (8) |
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5. In situ PCR with biotinylated primers |
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100 | (2) |
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102 | (1) |
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6. Primed in situ DNA synthesis (PRINS) |
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103 | (14) |
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103 | (1) |
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104 | (1) |
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104 | (11) |
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105 | (1) |
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The basic PRINS procedure |
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106 | (1) |
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107 | (3) |
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Variations on the basic method |
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110 | (5) |
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115 | (2) |
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7. Application of in situ PCR techniques to human tissues |
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117 | (22) |
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117 | (1) |
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2. Preparation of glass slides and tissues |
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118 | (3) |
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Glass slides with Teflon-edged wells |
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118 | (1) |
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Preparation of cells and tissues |
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119 | (2) |
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3. In situ amplification: DNA and RNA targets |
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121 | (10) |
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Basic preparation, all protocols |
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121 | (3) |
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Reverse transcriptase variation: in situ RNA amplification |
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124 | (7) |
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4. Special application of in situ amplification |
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131 | (1) |
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In situ amplification and immunohistochemistry |
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131 | (1) |
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Multiple signals, multiple labels in individual cells |
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131 | (1) |
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131 | (5) |
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Summary of the basic concepts of in situ hybridization |
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131 | (5) |
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6. Validation and controls |
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136 | (1) |
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137 | (2) |
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8. Applications and modifications of PCR in situ hybridization |
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139 | (24) |
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139 | (3) |
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139 | (1) |
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140 | (2) |
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2. Single parameter analysis |
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142 | (8) |
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142 | (4) |
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146 | (4) |
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3. Multiparameter analysis |
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150 | (2) |
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4. Fluorescence in situ 5'-nuclease assay and fluorescence detection |
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152 | (9) |
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161 | (2) |
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9. Automation of in situ amplification |
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163 | (32) |
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1. Technologies available for in situ amplification |
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163 | (1) |
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2. The GeneAmp(R) In Situ PCR System 1000 |
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164 | (10) |
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164 | (1) |
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PCR amplification in situ: problems and pitfalls |
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165 | (1) |
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In situ PCR: the case for dedicated instrumentation and sample containment systems |
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166 | (1) |
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A dedicated high-performance system for PCR amplification on glass slides |
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167 | (5) |
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Dedicated and qualified reagent system for in situ PCR amplification |
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172 | (2) |
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174 | (1) |
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3. Automation and the Omnislide System |
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174 | (19) |
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174 | (1) |
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Factors and problems to be addressed in order to semi-automate PCR ISH |
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175 | (2) |
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System design: theoretical and practical considerations |
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177 | (7) |
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184 | (3) |
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187 | (6) |
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193 | (1) |
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193 | (1) |
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193 | (2) |
A1. List of suppliers |
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195 | (6) |
Index |
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201 | |