Unravelling Single Cell Genomics -- Contents -- Chapter 1 An Introduction to Molecular Biology -- Abstract -- 1.1 DNA Structure and Gene Expression -- 1.2 Molecular Biology Tools for Nucleic Acid Studies -- 1.2.1 DNA Engineering -- 1.2.2 Polymerase Chain Reaction -- 1.2.3 DNA Microarrays -- References -- Chapter 2 The Central Dogma in Molecular Biology -- Abstract -- 2.1 Replication -- 2.2 Transcription -- 2.3 Translation -- 2.4 Regulation of Gene Expression -- 2.4.1 Transcriptional Control -- 2.4.2 Post-transcriptional Modifications -- 2.4.3 Translational Control -- 2.4.4 Post-translational Control -- 2.5 Limitations of the Central Dogma -- 2.6 Single Cells and their Complexity -- References -- Chapter 3 From Unicellular to Multicellular Organisms: Tells from Evolution and from Development -- Abstract -- 3.1 Cells from Evolution -- 3.2 Cells from Development -- References -- Chapter 4 Understanding Cellular Differentiation -- Abstract -- 4.1 Development of the Cerebral Cortex -- 4.2 Neuronal Differentiation -- 4.3 Single Cell Analysis in Differentiation Processes -- References -- Chapter 5 Realistic Models of Neurons Require Quantitative Information at the Single-cell Level -- Abstract -- 5.1 Introduction -- 5.2 The Importance of Precise Neuronal Morphology -- 5.3 Each Neuron has a Unique Neurochemistry -- 5.4 Conclusions -- References -- Chapter 6 Application to Cancerogenesis: Towards Targeted Cancer Therapies? -- Abstract -- 6.1 Molecular Diagnosis in Cancer -- 6.2 Detection and Malignant Origin of Disseminated Cancer Cells -- 6.3 Genomic Studies of Single Disseminated Cancer Cells -- 6.4 Oncogene Dependence and Tumor Suppressor Sensitivity in Metastasis Founder Cells -- References -- Chapter 7 Capturing a Single Cell -- Abstract -- 7.1 Introduction -- 7.2 Overview of Cell Sorting Technologies -- 7.3 Laser Capture Microdissection Technologies.

7.3.1 Infrared Laser Capture Systems -- 7.3.2 Ultraviolet Cutting Systems -- 7.4 Protocols Before Laser Microdissection (Tissue Sampling and Preparation) -- 7.4.1 Dissection from Fresh Frozen Tissue -- 7.4.2 Dissection from Formalin-fixed Paraffin-embedded Tissue -- 7.4.3 Immuno Laser Capture Microdissection -- 7.4.4 Other Cell-labeling Methods -- 7.5 Conclusion -- References -- Chapter 8 Looking at the DNA of a Single Cell -- Abstract -- 8.1 Challenges of Single Cell DNA Amplification -- 8.2 Methods for Amplifying Genomic DNA of Single Cells -- 8.3 Array Comparative Genomic Hybridization of Single Cells -- 8.4 Combined Genome and Transcriptome Analysis of Single Cells -- 8.5 Perspective on Single Cell DNA Analysis -- References -- Chapter 9 Gene Analysis of Single Cells -- Abstract -- 9.1 Single Cell RT-PCR After Patch Clamp -- 9.2 Correlating mRNA Expression and Functional Properties of Single Cells -- 9.3 Quantitative Analyses by scPCR -- 9.4 Molecular and Functional Phenotyping of Neuronal Types -- 9.5 Patch-clamp Harvesting of Single Cells -- 9.6 Sensitivity Limits -- 9.7 Controls -- 9.8 Interpretation of scPCR Results -- Conclusion -- Acknowledgement -- References -- Chapter 10 Proteomics -- Abstract -- 10.1 Motivation to Study Proteins at the Single Cell Level -- 10.1.1 Proteins, mRNAs and DNA -- 10.1.2 Sample Preparation -- 10.1.3 Sub-proteome Analysis -- 10.2 Analytical Strategies -- 10.2.1 Mass Spectrometry -- 10.2.2 Coupling Separation Techniques and Mass Spectrometry -- 10.3 Strategies for Studying Proteins in Low Amounts of Samples -- 10.3.1 How to Enhance the Sensitivity: Miniaturization, Integration, and Automation -- 10.3.2 MALDI Interfaces -- Conclusion -- References -- Chapter 11 Microfluidics: Basic Concepts and Microchip Fabrication -- Abstract -- 11.1 Size Matters: An Introduction.

11.2 A Short Chronology of Microfluidics Research -- 11.3 Microfluidics: Some Basics -- 11.3.1 Flow Generation -- 11.3.2 Laminar Flow -- 11.3.3 Digital Microfluidics: Segmented Flow -- 11.4 Fabrication Techniques and Materials -- 11.4.1 Photolithography -- 11.4.2 Soft Lithography -- 11.4.3 Microchip Materials -- 11.4.4 From Fabrication to Application -- 11.5 Concluding Remarks -- References -- Chapter 12 Cell Capture and Lysis on a Chip -- Abstract -- 12.1 Introduction -- 12.2 Cell Capture on a Chip -- 12.2.1 Mechanical Trapping -- 12.2.2 Electrical Trapping -- 12.2.3 Fluidic Trapping -- 12.2.4 Alternative Trapping Techniques -- 12.2.5 Conclusion on Cell Trapping -- 12.3 Cell Lysis in a Chip -- 12.3.1 Thermal Lysis -- 12.3.2 Chemical Lysis -- 12.3.3 ''Alkaline'' or Electrochemical Lysis -- 12.3.4 Electrical Lysis -- 12.3.5 Mechanical Lysis -- 12.3.6 Alternative Mechanical Lysis: Acoustic Lysis -- 12.3.7 Optical Lysis -- 12.3.8 Conclusion on Cell Lysis -- 12.4 Conclusion -- References -- Chapter 13 DNA Analysis in Microfluidic Devices and their Application to Single Cell Analysis -- Abstract -- 13.1 Amplification on a Chip -- 13.1.1 Polymerase Chain Reaction -- 13.1.2 Isothermal Techniques -- 13.2 DNA Analysis -- 13.2.1 Real-time PCR Detection -- 13.2.2 Capillary Electrophoresis -- 13.3 Why and When Smaller is Better -- 13.4 Applications of Microfluidic Single Cell Genetic Analysis in Microbial Ecology -- 13.5 Conclusion -- References -- Chapter 14 Gene Expression Analysis on Microchips -- Abstract -- 14.1 Introduction -- 14.2 Multi-step Microfluidic RT-PCR -- 14.3 One-step Microfluidic RNA Analysis -- 14.4 Microfluidic cDNA Analysis -- 14.5 Single Cell RNA Analysis -- 14.6 Conclusion -- Acknowledgement -- References -- Chapter 15 Analysis of Proteins at the Single Cell Level -- Abstract -- 15.1 Introduction -- 15.1.1 Protein Analysis: The Challenge.

15.1.2 Why Microfluidics? -- 15.1.3 Microfluidics and Protein Analysis -- 15.2 Electrospray Ionization Mass Spectrometry -- 15.2.1 Connections and Coupling -- 15.2.2 Sample Processing: Purification and Digestion -- 15.2.3 Integrated Systems -- 15.3 MALDI-MS -- 15.3.1 Microfabricated MALDI Targets -- 15.3.2 Off-line Sample Preparation -- 15.3.3 Integrated Microsystems -- 15.4 Innovative Approaches for Protein Analysis at the Single Cell Level -- 15.4.1 Invasive Analysis -- 15.4.2 Partially Invasive Analysis -- 15.4.3 Non-invasive Analysis -- 15.5 Conclusion and Perspectives -- References -- Chapter 16 A Concrete Case: A Microfluidic Device for Single Cell Whole Transcriptome Analysis -- Abstract -- 16.1 Introduction -- 16.2 Choice of Biological Protocol, Material and Fabrication Technique -- 16.2.1 Protocols for Single Cell Whole Transcriptome Analysis -- 16.2.2 Miniaturizing Reactions: Continuous Flows, Reaction Chambers or Droplet Micro-fluidic Reactions -- 16.2.3 Choosing the Microchip Material -- 16.2.4 Microchip Fabrication -- 16.3 Integrating Reverse Transcription on a Chip -- 16.3.1 Gene Expression Profiling of Single-Cell Scale Amounts of RNA -- 16.3.2 Gene Expression Profiling of Single Cells -- 16.4 Amplifying the Transcriptome on a Chip -- 16.5 Detecting the Transcriptome on a Chip -- 16.5.1 Microfluidics and Conventional Microarrays -- 16.5.2 Microarray Development Using DNA Immobilization onto Microchannels -- 16.5.3 Towards Transcriptome Analysis in the Liquid Phase -- 16.6 Some Practical Conclusions -- References -- Chapter 17 Tiny Droplets for High-throughput Cell-based Assays -- Abstract -- 17.1 Introduction -- 17.2 Droplet-based Microfluidics -- 17.2.1 EWOD and ''Digital Microfluidics'': Tools for High-content Screening -- 17.2.2 Droplet-based Microfluidics: Tools for High-throughput Screening.

17.3 Generating and Manipulating Droplets -- 17.3.1 Droplet Production -- 17.3.2 Droplet Division -- 17.3.3 Droplet Flow, Droplet Synchronization, and Droplet Incubation -- 17.3.4 Droplet Content Detection and Droplet Sorting -- 17.4 In Vitro Compartmentalization of Biological Reactions -- 17.4.1 Cell Compartmentalization in Aqueous Droplets -- 17.4.2 Incubation and Cell Viability in Droplets -- 17.4.3 Cell-based Assays and Cell Manipulation -- 17.5 Towards Integrated Platforms for Cell-based Assays -- 17.6 Conclusions -- References -- Chapter 18 New Detection Methods for Single Cells -- Abstract -- 18.1 Introduction -- 18.2 Bio-barcode Strategy -- 18.2.1 Principle -- 18.2.2 An Example: DNA Origami -- 18.3 Imaging Gene Expression in Living Cells -- 18.3.1 Motivations -- 18.3.2 Improvements in Photonic Microscopy -- 18.3.3 Improvements in Fluorophore Design -- 18.4 Quantum Dots-based Techniques -- 18.4.1 Quantum Dots Bead-based Assays -- 18.4.2 Single Quantum Dots-based DNA Nanosensors -- 18.4.3 Quantum Dots for Super-resolution Microscopy -- 18.5 Gold Nanoparticle-based Detection Methods -- 18.5.1 Resonant Light Scattering Detection -- 18.5.2 Molecular Beacons with Gold Nanoparticles -- 18.5.3 Molecular Plasmonic Rulers -- 18.5.4 Surface-enhanced Raman Scattering Detection -- 18.6 Electrochemical Sensors -- 18.7 Concluding Remarks -- References -- Subject Index.