Functional genomics : methods and protocols / edited by Michael Kaufmann and Claudia Klinger. — 2nd ed. — New York : Springer, c2012. – (58.17/M592/v.815)

Contents

    Contents
    
    Preface
    Contributors
    PART I BIOINFORMATICS
    1 Prediction of Protein Tertiary Structures Using MUFOLD
    2 Prediction of Protein Functions
    3 Genome-Wide Screens for Expressed Hypothetical Proteins
    4 Self-Custom-Made SFP Arrays for Nonmodel Organisms
    PART II DNA ANALYSIS
    5 Construction and Analysis of Full-Length and Normalized cDNA Libraries from Citrus 51
    6 Assembling Linear DNA Templates for In Vitro Transcription and Translation
    7 Automated Computational Analysis of Genome-Wide DNA Methylation Profiling Data from HELP-Tagging Assays
    PART III RNA ANALYSIS
    8 Detection of RNA Editing Events in Human Cells Using High-Throughput Sequencing
    9 Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization
    10 Whole-Genome RT-qPCR MicroRNA Expression Profiling 121
    11 Using Quantitative Real-Time Reverse Transcriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG 131
    12 FRET-Based Real-Time DNA Microarrays 147
    PART IV PROTEIN ANALYSIS I: QUANTIFICATION AND IDENTIFICATION
    13 2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps
    14 The Use of Antigen Microarrays in Antibody Profiling 175
    15 Limited Proteolysis in Proteomics Using Protease-Immobilized Microreactors
    16 Mass Spectrometry for Protein Quantification in Biomarker Discovery 199
    PART V PROTEIN ANALYSIS II: FUNCTIONAL CHARACTERIZATION
    17 High-Throughput Microtitre Plate-Based Assay for DNA Topoisomerases 229
    18 Microscale Thermophoresis as a Sensitive Method to Quantify Protein: Nucleic Acid Interactions in Solution 241
    19 Bioluminescence Resonance Energy Transfer: An Emerging Tool for the Detection of Protein-Protein Interaction in Living Cells 253
    20 LuMPIS: Luciferase-Based MBP-PuI1-Down Protein Interaction Screening System
    21 Yeast Two-Hybrid Screens: Improvement of Array-Based Screening Results by N- and C-terminally Tagged Fusion Proteins 277
    22 Inducible microRNA-Mediated Knockdown of the Endogenous Human Lamin A/C Gene
    23 Multiple-Gene Silencing Using Antisense RNAs in Escherichia coli 307
    24 Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and In Situ Hybridization
    25 Silencing of Gene Expression by Gymnotic Delivery of Antisense Oligonucleotides
    26 Polycistronic Expression of Interfering RNAs from RNA Polymerase III Promoters
    PART VI METABOLITE ANALYSIS
    27 Metabolite Analysis of Cannabis sativa L. by NMR Spectroscopy
    28 Metabolome Analysis of Gram-Positive Bacteria such as Staphylococcus aureus by GC-MS and LC-MS
    29 Metabolic Fingerprinting Using Comprehensive Two-Dimensional Gas Chromatography - Time-of-Flight Mass Spectrometry 399
    Index 413