Droplet microfluidics for single cell and nucleic acid analysis

...................................................................................................................... 3 List of publications and manuscript ......................................................................... 9 Contributions to the publications ........................................................................... 10 Table of contents ...................................................................................................... 11 Thesis outline ............................................................................................................ 13 Chapter 1 Droplet microfluidics ............................................................................ 15 1.1 Microfluidic chip fabrication ........................................................................... 15 1.2 Surfactants ........................................................................................................ 16 1.3 Unit operations ................................................................................................. 17 1.3.1 Droplet generation ..................................................................................... 17 1.3.2 Droplet manipulation ................................................................................ 18 Droplet fission .................................................................................................... 18 Droplet fusion .................................................................................................... 19 Droplet incubation .............................................................................................. 20 Droplet sorting ................................................................................................... 20 1.3.3 Droplet content analysis ............................................................................ 21 1.4 Single particle encapsulation in droplets .......................................................... 22 1.5 Applications of acoustics in droplet microfluidics ........................................... 23 Chapter 2 Droplet microfluidics for biological analysis ...................................... 24 2.1 Droplet based mammalian cell analysis ........................................................... 24 2.2 Droplet based nucleic acid analysis ................................................................. 26 2.2.1 Droplet PCR .............................................................................................. 26 2.2.2 Detection of rare mutations ....................................................................... 28 2.2.3 Target enrichment for next-generation sequencing ................................... 29 2.2.4 Single cell genomic and transcriptomic analysis ...................................... 30 2.2.5 Other applications ..................................................................................... 32 Chapter 3 Present investigation ............................................................................. 34 Paper I: Automated analysis of dynamic behavior of single cells in picoliter droplets ................................................................................................................... 35 Paper II: Droplet size influences division of mammalian cell factories in droplet microfluidic cultivation .......................................................................................... 38 Droplet microfluidics for single cell and nucleic acid analysis 12 Paper III: Color-coded bead based readout from droplet PCR for the detection of pathogen biomarkers ............................................................................................... 41 Paper IV: Controlled lateral positioning of microparticles inside droplets using acoustophoresis ....................................................................................................... 44 Chapter 4 Concluding remarks .............................................................................. 47 Abbreviations ............................................................................................................ 49 Acknowledgements ................................................................................................... 50 References .................................................................................................................. 52 Publications and manuscript ................................................................................... 58 Prem Kumar Periyannan Rajeswari