Useful for all scientists who plan to establish or extend one of the technologies described in the book in their own labs.
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the tranillegalscriptome, proteome and metabolome, respectively.Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.
Part I: Bioinformatics
1. Prediction of Protein Tertiary Structures using MUFOLD
Jingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan Kosztin, Yi Shang, and Dong Xu
2. Prediction of Protein Functions
Roy D. Sleator
3. Genome Wide Screens for Expressed Hypothetical Proteins
Claus Desler, Jon Ambaek Durhuus and Lene Juel Rasmussen
4. Self Custom-Made SFP Arrays for Non-Model Organisms
Ron Ophir and Amir Sherman
Part II: DNA Analysis
5. Construction and Analysis of Full-length and Normalized cDNA Libraries from Citrus
M Carmen Marques and Miguel A Perez-Amador
6. Assembling Linear DNA Templates for In vitro Tranillegalscription and Translation
Viktor Stein, Miriam Kaltenbach and Florian Hollfelder
7. Automated Computational Analysis of Genome-wide DNA Methylation Profiling Data from HELP-tagging Assays
Qiang Jing, Andrew McLellan, John M. Greally and Masako Suzuki
Part III: RNA Analysis
8. Detecting of RNA Editing Events in Human Cells using High-Throughput Sequencing
Iouri Chepelev
9. Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization
Ruisheng An and Parwinder S. Grewal
10. Whole Genome RT-qPCR MicroRNA Expression Profiling
Pieter Mestdagh, Stefaan Derveaux, Jo Vandesompele
11. Using Quantitative Real-Time Reverse Tranillegalscriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG
Siva Kumar Panguluri and Sham S. Kakar
12. FRET-Based Real-Time DNA Microarrays
Arjang Hassibi, Haris Vikalo, José Riechmann and Babak Hassibi
Part IV: Protein Analysis I: Quantification and Indentification
13. 2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps
Maria Paola Simula, Agata Notarpietro, Giuseppe Toffoli, and Valli De Re
14. The Use of Antigen Microarrays in Antibody Profiling
Krisztián Papp and József Prechl
15. Limited Proteolysis in Proteomics using Protease-immobilized Microreactors
Hiroshi Yamaguchi, Masaya Miyazaki and Hideaki Maeda
16. Mass Spectrometry for Protein Quantification in Biomarker Discovery
Mu Wang and Jinsam You
Part V: Protein Analysis II: Functional Characterization
17. High-throughput Microtitre Plate-based Assay for DNA Topoisomerases
James A Taylor, Nicolas P Burton and Anthony Maxwell
18. Microscale Thermophoresis as a Sensitive Method to Quantify Protein-Nucleic Acid Interactions in Solutions
Karina Zillner, Moran Jerabek-Willemsen, Stefan Duhr, Dieter Braun, Gernot Längst and Philipp Baaske
19 Bioluminescence Resonance Energy Transfer: an Emerging Tool for the Detection of Protein-protein Interaction in Living Cells
Søren W. Gersting, Amelie S. Lotz-Havla and Ania C. Muntau
20 LuMPIS – Luciferase-based MBP-pull-down Protein Interaction Screening System
María G. Vizoso Pinto and Armin Baiker
21 Yeast Two-Hybrid Screens: Improvement of Array-based Screening Results by N- and C-terminally Tagged Fusion Proteins
Thorsten Stellberger, Roman Häuser, Peter Uetz, and Albrecht von Brunn
22. Inducible microRNA-mediated Knockdown of the Endogenous Human Lamin A/C Gene
Ina Weidenfeld
23. Multiple-gene Silencing using Antisense RNAs in Escherichia Coli
Nobutaka Nakashima, Shan Goh, Liam Good and Tomohiro Tamura
24. Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and in Situ Hybridization
William Ka Fai Tse and Yun-Jin Jiang
25. Silencing of Gene Expression by Gymnotic Delivery of Antisense Oligonucleotides
Harris S. Soifer, Troels Koch, Johnathan Lai, Bo Hansen, Anja Hoeg, Henrik Oerum and C.A. Stein
26. Polycistronic Expression of Interfering RNAs and RNA Plymerase III Promoters
Laura F. Steel and Viraj R. Sanghvi
Part VI: Metabolite Analysis
27. Metabolite Analysis of Cannabis sativa L. by NMR Spectroscopy
Isvett Josefina Flores-Sanchez, Young Hae Choi and Robert Verpoorte
28. Metabolome Analysis of Grame-positive Bacteria such as Staphylococcus aureus by GC-MS and LC MS
Manuel Liebeke, Kirsten Dörries, Hanna Meyer and Micheal Lalk
29. Metabolic Fingerprinting Using Comprehensive Two-dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry(GCxGX-TOF-MS)
Martin F. Almstetter, Peter J. Oefner, and Katja Dettmer
In the last decade the life sciences have evolved at a startling rate, culminating in today's high-throughput methods in biochemistry laboratories. In this book, expert researchers focus on dynamic aspects of the tranillegalscriptome, proteome and metabolome.
Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the tranillegalscriptome, proteome and metabolome, respectively.Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.
Prediction of Protein Tertiary Structures using MUFOLD.-Prediction of Protein Functions.-Genome Wide Screens for Expressed Hypothetical Proteins.-Self Custom-Made SFP Arrays for Non-Model Organisms.-Construction and Analysis of Full-length and Normalized cDNA Libraries from Citrus.-Assembling Linear DNA Templates for in vitro Tranillegalscription and Translation.-Automated Computational Analysis of Genome-wide DNA Methylation Profiling Data from HELP-tagging Assays.-Detection of RNA Editing Events in Human Cells using High- Throughput Sequencing.-Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization.-Whole Genome RT-qPCR MicroRNA Expression Profiling.-Using Quantitative Real-Time Reverse Tranillegalscriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG.-FRET-Based Real-Time DNA Microarrays.- 2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps.-The use of Antigen Microarrays in Antibody Profiling.-Limited Proteolysis in Proteomics using Protease-immobilized Microreactors.-Mass Spectrometry for Protein Quantification in Biomarker Discovery.-High-throughput Microtitre Plate-based Assay for DNA Topoisomerases.-Microscale Thermophoresis as a Sensitive Method to Quantify Protein - Nucleic Acid Interactions in Solution.-Bioluminescence Resonance Energy Transfer: an Emerging Tool for the Detection of Protein-protein Interaction in Living Cells.-LuMPIS - Luciferase-based MBP-pull-down Protein Interaction Screening System.-Yeast Two-Hybrid Screens: Improvement of Array-based Screening Results by N- and C-terminally Tagged Fusion Proteins.-Inducible microRNA-mediated Knockdown of the Endogenous Human Lamin A/C Gene.- Multiple-gene Silencing using Antisense RNAs in Escherichia coli.-Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and in situ Hybridization.-Silencing of Gene Expression by GymnoticDelivery of Antisense Oligonucleotides.-Polycistronic Expression of Interfering RNAs from RNA Polymerase III Promoters.-Metabolite Analysis of Cannabis sativa L. by NMR Spectroscopy.-Metabolome Analysis of Gram-positive Bacteria such as Staphylococcus aureus by GC-MS and LC-MS.-Metabolic Fingerprinting Using Comprehensive Two-dimensional Gas Chromatography - Time-of-flight Mass Spectrometry (GC×GC-TOF-MS).
Inhaltsverzeichnis
Part I: Bioinformatics
1. Prediction of Protein Tertiary Structures using MUFOLD
Jingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan Kosztin, Yi Shang, and Dong Xu
2. Prediction of Protein Functions
Roy D. Sleator
3. Genome Wide Screens for Expressed Hypothetical Proteins
Claus Desler, Jon Ambaek Durhuus and Lene Juel Rasmussen
4. Self Custom-Made SFP Arrays for Non-Model Organisms
Ron Ophir and Amir Sherman
Part II: DNA Analysis
5. Construction and Analysis of Full-length and Normalized cDNA Libraries from Citrus
M Carmen Marques and Miguel A Perez-Amador
6. Assembling Linear DNA Templates for In vitro Tranillegalscription and Translation
Viktor Stein, Miriam Kaltenbach and Florian Hollfelder
7. Automated Computational Analysis of Genome-wide DNA Methylation Profiling Data from HELP-tagging Assays
Qiang Jing, Andrew McLellan, John M. Greally and Masako Suzuki
Part III: RNA Analysis
8. Detecting of RNA Editing Events in Human Cells using High-Throughput Sequencing
Iouri Chepelev
9. Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization
Ruisheng An and Parwinder S. Grewal
10. Whole Genome RT-qPCR MicroRNA Expression Profiling
Pieter Mestdagh, Stefaan Derveaux, Jo Vandesompele
11. Using Quantitative Real-Time Reverse Tranillegalscriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG
Siva Kumar Panguluri and Sham S. Kakar
12. FRET-Based Real-Time DNA Microarrays
Arjang Hassibi, Haris Vikalo, José Riechmann and Babak Hassibi
Part IV: Protein Analysis I: Quantification and Indentification
13. 2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps
Maria Paola Simula, Agata Notarpietro, Giuseppe Toffoli, and Valli De Re
14. The Use of Antigen Microarrays in Antibody Profiling
Krisztián Papp and József Prechl
15. Limited Proteolysis in Proteomics using Protease-immobilized Microreactors
Hiroshi Yamaguchi, Masaya Miyazaki and Hideaki Maeda
16. Mass Spectrometry for Protein Quantification in Biomarker Discovery
Mu Wang and Jinsam You
Part V: Protein Analysis II: Functional Characterization
17. High-throughput Microtitre Plate-based Assay for DNA Topoisomerases
James A Taylor, Nicolas P Burton and Anthony Maxwell
18. Microscale Thermophoresis as a Sensitive Method to Quantify Protein-Nucleic Acid Interactions in Solutions
Karina Zillner, Moran Jerabek-Willemsen, Stefan Duhr, Dieter Braun, Gernot Längst and Philipp Baaske
19 Bioluminescence Resonance Energy Transfer: an Emerging Tool for the Detection of Protein-protein Interaction in Living Cells
Søren W. Gersting, Amelie S. Lotz-Havla and Ania C. Muntau
20 LuMPIS - Luciferase-based MBP-pull-down Protein Interaction Screening System
María G. Vizoso Pinto and Armin Baiker
21 Yeast Two-Hybrid Screens: Improvement of Array-based Screening Results by N- and C-terminally Tagged Fusion Proteins
Thorsten Stellberger, Roman Häuser, Peter Uetz, and Albrecht von Brunn
22. Inducible microRNA-mediated Knockdown of the Endogenous Human Lamin A/C Gene
Ina Weidenfeld
23. Multiple-gene Silencing using Antisense RNAs in Escherichia Coli
Nobutaka Nakashima, Shan Goh, Liam Good and Tomohiro Tamura
24. Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and in Situ Hybridization
William Ka Fai Tse and Yun-Jin Jiang
25. Silencing of Gene Expression by Gymnotic Delivery of Antisense Oligonucleotides
Harris S. Soifer, Troels Koch, Johnathan Lai, Bo Hansen, Anja Hoeg, Henrik Oerum and C.A. Stein
26. Polycistronic Expression of Interfering RNAs and RNA Plymerase III Promoters
Laura F. Steel and Viraj R. Sanghvi
Part VI: Metabolite Analysis
27. Metabolite Analysis of Cannabis sativa L. by NMR Spectroscopy
Isvett Josefina Flores-Sanchez, Young Hae Choi and Robert Verpoorte
28. Metabolome Analysis of Grame-positive Bacteria such as Staphylococcus aureus by GC-MS and LC MS
Manuel Liebeke, Kirsten Dörries, Hanna Meyer and Micheal Lalk
29. Metabolic Fingerprinting Using Comprehensive Two-dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry(GCxGX-TOF-MS)
Martin F. Almstetter, Peter J. Oefner, and Katja Dettmer
Klappentext
Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the tranillegalscriptome, proteome and metabolome, respectively.Written in the highly successful Methods in Molecular Biology¿ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.nAuthoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.
Useful for all scientists who plan to establish or extend one of the technologies described in the book in their own labs.
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
Includes supplementary material: sn.pub/extras
