Genomes and Gene Expression in Individual Cells

Abstract

I present several technology developments and scientific contributions in this thesis. I first introduce Microbe-seq, a method we developed to obtain single microbe genomes at high throughput by droplet microfluidics. We develop an experimental workflow that incorporates cell encapsulation, lysis, whole genome amplification, tagmentation, and barcoding inside droplets which can be manipulated as reaction chambers at kilohertz speed, thereby achieving high throughput. We apply Microbe-seq to samples from one healthy human subject and acquire 21,914 single cell genomes. With these single cell genomes, we assemble 93 species-level assembled genomes, including 15 genomes of novel species. These single cell genomes also allow us to reveal subspecies level microbial diversities in the human gut microbiome. Then, I present the study of viral infection by inDrop, a method to profile gene expression with single cell resolution at high throughput with droplet microfluidics. We use inDrop to examine single cell transcriptomics of cultured primary human cells infected by BKV, a prevalent human virus that can cause diseases in immunosuppressed people. We confirm that cells with the same type response differently from BKV infection. We identify genes that are responsible for restricted or aborted infection in some cell subpopulations. Finally, I describe an approach to mass produce double emulsions with tandem emulsification, a two-step process with droplet microfluidic devices. With this method, single emulsions are generated in a first device and are re-injected directly into a second device to form uniform double emulsions. Since wettability requirements are spatially separated into two devices, we can robustly functionalize these devices. Thus, a lot dropmakers can be parrallized into a set of devices. We demonstrate the application of tandem emulsification for scalable core-shell emulsion production with both integrated flow focusing or millipede devices.