Content: Machine generated contents note: ch. 1 An Introduction to Molecular Biology / Luce Dauphinot — 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 — ch. 2 The Central Dogma in Molecular Biology / Laili Mahmoudian — 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 — ch. 3 From Unicellular to Multicellular Organisms: Tells from Evolution and from Development / Tania Vitalis — Abstract — 3.1. Cells from Evolution — 3.2. Cells from Development — References — ch. 4 Understanding Cellular Differentiation / Tania Vitalis — Abstract 4.1. Development of the Cerebral Cortex — 4.2. Neuronal Differentiation — 4.3. Single Cell Analysis in Differentiation Processes — References — ch. 5 Realistic Models of Neurons Require Quantitative Information at the Single-cell Level / Nicolas Le Novere — Abstract — 5.1. Introduction — 5.2. The Importance of Precise Neuronal Morphology — 5.3. Each Neuron has a Unique Neurochemistry — 5.4. Conclusions — References — ch. 6 Application to Cancerogenesis: Towards Targeted Cancer Therapies? / Christoph A. Klein — 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 — ch. 7 Capturing a Single Cell / Joel Lachuer — 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 — ch. 8 Looking at the DNA of a Single Cell / Christoph A. Klein — 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 — ch. 9 Gene Analysis of Single Cells / Bertrand Lambolez — 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 — ch. 10 Proteomics / Joelle Vinh — 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 — ch. 11 Microfluidics: Basic Concepts and Microchip Fabrication / Petra S. Dittrich — 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 — ch. 12 Cell Capture and Lysis on a Chip / Albert van den Berg — 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 — ch. 13 DNA Analysis in Microfluidic Devices and their Application to Single Cell Analysis / Angelique Le Bras — 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 — ch. 14 Gene Expression Analysis on Microchips / Max Chahert — 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 — ch. 15 Analysis of Proteins at the Single Cell Level / Severine Le Gac — 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 — ch. 16 A Concrete Case: A Microfluidic Device for Single Cell Whole Transcriptome Analysis / Marie-Claude Potier — 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 — ch. 17 Tiny Droplets for High-throughput Cell-based Assays / V. Taly — 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 — ch. 18 New Detection Methods for Single Cells / Emmanuel Fort — 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