Dissection of Tissue Components. Manual Microdissection... Valentina Faoro and Giorgio Stanta
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1 Part I Archive Tissues 1 Archive Tissues Giorgio Stanta 3 2 Preanalytical Time Interval (PATI) and Fixation Lorenzo Daniele, Giuseppe D Armento, and Gianni Bussolati 5 3 Formalin-Free Fixatives Isabella Dotti, Serena Bonin, Giorgio Basili, and Valentina Faoro 13 Part II Dissection of Tissue Components 4 Manual Microdissection Tissue Microarray (TMA) Valentina Faoro and Anna Sapino 23 6 Laser Capture Microdissection (LCM) Elvira Stacher, Hannelore Kothmaier, Iris Halbwedl, 27 Part III Extraction, Purification, Quantification and Quality Assessment of Nucleic Acids 7 DNA Extraction from Formalin-Fixed Paraffin-Embedded (FFPE) Tissues Serena Bonin, Patricia J.T.A. Groenen, Iris Halbwedl, 8 DNA Extraction from Formalin-Fixed Paraffin-Embedded Tissues (FFPE) (from Small Fragments of Tissues or Microdissected Cells) Serena Bonin, Patricia J.T.A. Groenen, Iris Halbwedl, vii
2 viii 9 Fast Protocol for DNA Extraction from Formalin-Fixed Paraffin-Embedded Tissues Falk Hlubek and Andreas Jung DNA Extraction from Blood and Forensic Samples Solange Sorçaburu Cigliero, Elisabetta Edalucci, and Paolo Fattorini Restoration and Reconstruction of DNA Length Serena Bonin and Federica Tavano RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissues Serena Bonin and Giorgio Stanta 13 RNA Extraction from Decalcified and Non-decalcified Formalin-Fixed Paraffin-Embedded Tissues Marco Alberghini, Stefania Benini, Gabriella Gamberi, Stefania Cocchi, and Licciana Zanella 14 RNA Temperature Demodification Serena Bonin and Giorgio Stanta MicroRNA Extraction from Formalin-Fixed Paraffin-Embedded Tissues Roberto Cirombella and Andrea Vecchione Quantification of Nucleic Acids Isabella Dotti and Serena Bonin Integrity Assessment of Nucleic Acids Isabella Dotti and Serena Bonin DNase Treatment of RNA Isabella Dotti and Serena Bonin 87 Part IV 19 Reverse Transcription (RT) Reverse Transcription Isabella Dotti, Serena Bonin, and Ermanno Nardon 93 Part V Nucleic Acid Amplification 20 General Protocol for End-Point PCR Quantitative End-Point PCR
3 ix 22 Nested-PCR General Protocol for Dot-Blot PCR-ELISA Christiane Schewe, Wilko Weichert, and Manfred Dietel Quantitative Real-Time RT-PCR Isabella Dotti, Ermanno Nardon, Danae Pracella, and Serena Bonin 121 Part VI DNA Sequencing 26 DNA Sequencing from PCR Products Giorgio Basili, Serena Bonin, and Isabella Dotti Pyrosequencing Analysis for Detection of KRAS Mutation Gerlinde Winter and Gerald Höfler 143 Part VII Microsatellite Analysis 28 Microsatellite Instability (MSI) Detection in DNA from FFPE Tissues Damjan Glavac and Ermanno Nardon 29 General Protocol for Loss of Heterozygosity Detection Damjan Glavac and Ermanno Nardon Part VIII Methylation Analysis Qualitative Methylation Status Assessment Damjan Glavac and Ermanno Nardon Quantitative Methylation Status Assessment in DNA from FFPE Tissues with Bisulfite Modification and Real-Time Quantitative MSP Ermanno Nardon Part IX Analysis of Copy Number Variations 32 Comparative Genomic Hybridisation (CGH) Hannelore Kothmaier, Elvira Stacher, Iris Halbwedl, Multiplex Ligation-dependent Probe Amplification (MLPA) Ana Pilar Berbegall, Eva Villamón, Samuel Navarro, and Rosa Noguera 215
4 x 34 Fluorescence In Situ Hybridization (FISH) on Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Sections Marta Piqueras, Manish Mani Subramaniam, Samuel Navarro, Nina Gale, and Rosa Noguera Part X Microarrays 35 Introduction on Genome-wide Expression Profiling from Formalin-Fixed Paraffin-Embedded Tissues Using Microarrays Manfred Dietel, Jan Budczies, Wilko Weichert, and Carsten Denkert Part XI 36 Protein Extraction in Archive Tissues Introduction Protein Extraction from Formalin-Fixed Paraffin-Embedded Tissues Karl-Friedrich Becker and Christina Schott 38 Rapid Protein Extraction from Formalin-Fixed Paraffin-Embedded Tissue Samples Protein Extraction Protocol from Tissues Treated with Formalin-Free Fixatives Trichloroacetic Acid (TCA) Precipitation of Proteins Part XII Protein Electrophoretic Separation 41 One-Dimensional Sodium-Dodecyl-Sulfate (SDS) Polyacrylamide Gel Electrophoresis Visualization of Proteins Part XIII 265 Protein Immunodetection 43 Western Blotting Dot Blot
5 xi 45 Membrane Stripping Reverse-Phase Protein Microarrays Christina Schott and Karl-Friedrich Becker 279 Part XIV 47 Mass Spectrometry Introduction Valentina Faoro, Giorgio Stanta, and Alessandro Vindigni Sample Preparation and In Gel Tryptic Digestion for Mass Spectrometry Experiments MALDI Imaging Mass Spectrometry on Formalin-Fixed Paraffin-Embedded Tissues Axel Walch, Sandra Rauser, and Heinz Höfler Part XV Elements of Good Laboratory Practice 50 Introduction Giorgio Stanta, Ermanno Nardon, and Renzo Barbazza Internal Quality Control (IQC) Organization Giorgio Stanta, Ermanno Nardon, and Renzo Barbazza Standards for Equipment and Reagents Ermanno Nardon and Renzo Barbazza 309 Appendices Index
6
Guidelines for Molecular Analysis in Archive Tissues
Guidelines for Molecular Analysis in Archive Tissues Giorgio Stanta (Editor) Guidelines for Molecular Analysis in Archive Tissues Editor Prof. Dr. Giorgio Stanta Department of Medical Sciences University
Index 311. overview, 84, 85 pretreatment, 85 probe preparation, 85 washing, 85, 91. G GeneChip, see DNA microarray
Index 309 Index A AIDS, see Human immunodeficiency virus Allelotyping, microdissection advantages, 69, 70 ovarian cancer, data acquisition and analysis, 74 DNA extraction, 72, 73, 76 materials, 70, 71
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