Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells

It has long been the dream of biologists to map gene expression at the single-cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single-cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after leukemia inhibitory factor (LIF) withdrawal. The reproducibility of these high-throughput single-cell data allowed us to deconstruct cell populations and infer gene expression relationships. VIDEO ABSTRACT.

Colloidosomes: selectively permeable capsules composed of colloidal particles

We present an approach to fabricate solid capsules with precise control of size, permeability, mechanical strength, and compatibility. The capsules are fabricated by the self-assembly of colloidal particles onto the interface of emulsion droplets. After the particles are locked together to form elastic shells, the emulsion droplets are transferred to a fresh continuous-phase fluid that is the same as that inside the droplets. The resultant structures, which we call "colloidosomes," are hollow, elastic shells whose permeability and elasticity can be precisely controlled. The generality and robustness of these structures and their potential for cellular immunoisolation are demonstrated by the use of a variety of solvents, particles, and contents.

Monodisperse Double Emulsions Generated from a Microcapillary Device

Double emulsions are highly structured fluids consisting of emulsion drops that contain smaller droplets inside. Although double emulsions are potentially of commercial value, traditional fabrication by means of two emulsification steps leads to very ill-controlled structuring. Using a microcapillary device, we fabricated double emulsions that contained a single internal droplet in a core-shell geometry. We show that the droplet size can be quantitatively predicted from the flow profiles of the fluids. The double emulsions were used to generate encapsulation structures by manipulating the properties of the fluid that makes up the shell. The high degree of control afforded by this method and the completely separate fluid streams make this a flexible and promising technique.

Three-dimensional direct imaging of structural relaxation near the colloidal glass transition

Confocal microscopy was used to directly observe three-dimensional dynamics of particles in colloidal supercooled fluids and colloidal glasses. The fastest particles moved cooperatively; connected clusters of these mobile particles could be identified; and the cluster size distribution, structure, and dynamics were investigated. The characteristic cluster size grew markedly in the supercooled fluid as the glass transition was approached, in agreement with computer simulations; at the glass transition, however, there was a sudden drop in their size. The clusters of fast-moving particles were largest near the alpha-relaxation time scale for supercooled colloidal fluids, but were also present, albeit with a markedly different nature, at shorter beta-relaxation time scales, in both supercooled fluid and glass colloidal phases.

Single-cell analysis and sorting using droplet-based microfluidics

We present a droplet-based microfluidics protocol for high-throughput analysis and sorting of single cells. Compartmentalization of single cells in droplets enables the analysis of proteins released from or secreted by cells, thereby overcoming one of the major limitations of traditional flow cytometry and fluorescence-activated cell sorting. As an example of this approach, we detail a binding assay for detecting antibodies secreted from single mouse hybridoma cells. Secreted antibodies are detected after only 15 min by co-compartmentalizing single mouse hybridoma cells, a fluorescent probe and single beads coated with anti-mouse IgG antibodies in 50-pl droplets. The beads capture the secreted antibodies and, when the captured antibodies bind to the probe, the fluorescence becomes localized on the beads, generating a clearly distinguishable fluorescence signal that enables droplet sorting at ∼200 Hz as well as cell enrichment. The microfluidic system described is easily adapted for screening other intracellular, cell-surface or secreted proteins and for quantifying catalytic or regulatory activities. In order to screen ∼1 million cells, the microfluidic operations require 2-6 h; the entire process, including preparation of microfluidic devices and mammalian cells, requires 5-7 d.

Elastic behavior of cross-linked and bundled actin networks

Networks of cross-linked and bundled actin filaments are ubiquitous in the cellular cytoskeleton, but their elasticity remains poorly understood. We show that these networks exhibit exceptional elastic behavior that reflects the mechanical properties of individual filaments. There are two distinct regimes of elasticity, one reflecting bending of single filaments and a second reflecting stretching of entropic fluctuations of filament length. The mechanical stiffness can vary by several decades with small changes in cross-link concentration, and can increase markedly upon application of external stress. We parameterize the full range of behavior in a state diagram and elucidate its origin with a robust model.

Massively parallel single-nucleus RNA-seq with DroNc-seq

Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.

Novel Colloidal Interactions in Anisotropic Fluids

Small water droplets dispersed in a nematic liquid crystal exhibit a novel class of colloidal interactions, arising from the orientational elastic energy of the anisotropic host fluid. These interactions include a short-range repulsion and a long-range dipolar attraction, and they lead to the formation of anisotropic chainlike structures by the colloidal particles. The repulsive interaction can lead to novel mechanisms for colloid stabilization.

Droplet microfluidics for high-throughput biological assays

Droplet microfluidics offers significant advantages for performing high-throughput screens and sensitive assays. Droplets allow sample volumes to be significantly reduced, leading to concomitant reductions in cost. Manipulation and measurement at kilohertz speeds enable up to 10(8) samples to be screened in one day. Compartmentalization in droplets increases assay sensitivity by increasing the effective concentration of rare species and decreasing the time required to reach detection thresholds. Droplet microfluidics combines these powerful features to enable currently inaccessible high-throughput screening applications, including single-cell and single-molecule assays.

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

Chromatin profiling provides a versatile means to investigate functional genomic elements and their regulation. However, current methods yield ensemble profiles that are insensitive to cell-to-cell variation. Here we combine microfluidics, DNA barcoding and sequencing to collect chromatin data at single-cell resolution. We demonstrate the utility of the technology by assaying thousands of individual cells, and using the data to deconvolute a mixture of ES cells, fibroblasts and hematopoietic progenitors into high-quality chromatin state maps for each cell type. The data from each single cell is sparse, comprising on the order of 1000 unique reads. However, by assaying thousands of ES cells, we identify a spectrum of sub-populations defined by differences in chromatin signatures of pluripotency and differentiation priming. We corroborate these findings by comparison to orthogonal single-cell gene expression data. Our method for single-cell analysis reveals aspects of epigenetic heterogeneity not captured by transcriptional analysis alone.

Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity

We describe a highly efficient microfluidic fluorescence-activated droplet sorter (FADS) combining many of the advantages of microtitre-plate screening and traditional fluorescence-activated cell sorting (FACS). Single cells are compartmentalized in emulsion droplets, which can be sorted using dielectrophoresis in a fluorescence-activated manner (as in FACS) at rates up to 2000 droplets s(-1). To validate the system, mixtures of E. coli cells, expressing either the reporter enzyme beta-galactosidase or an inactive variant, were compartmentalized with a fluorogenic substrate and sorted at rates of approximately 300 droplets s(-1). The false positive error rate of the sorter at this throughput was <1 in 10(4) droplets. Analysis of the sorted cells revealed that the primary limit to enrichment was the co-encapsulation of E. coli cells, not sorting errors: a theoretical model based on the Poisson distribution accurately predicted the observed enrichment values using the starting cell density (cells per droplet) and the ratio of active to inactive cells. When the cells were encapsulated at low density ( approximately 1 cell for every 50 droplets), sorting was very efficient and all of the recovered cells were the active strain. In addition, single active droplets were sorted and cells were successfully recovered.

Collective cell guidance by cooperative intercellular forces

Cells comprising a tissue migrate as part of a collective. How collective processes are coordinated over large multi-cellular assemblies has remained unclear, however, because mechanical stresses exerted at cell-cell junctions have not been accessible experimentally. We report here maps of these stresses within and between cells comprising a monolayer. Within the cell sheet there arise unanticipated fluctuations of mechanical stress that are severe, emerge spontaneously, and ripple across the monolayer. Within that stress landscape, local cellular migrations follow local orientations of maximal principal stress. Migrations of both endothelial and epithelial monolayers conform to this behaviour, as do breast cancer cell lines before but not after the epithelial-mesenchymal transition. Collective migration in these diverse systems is seen to be governed by a simple but unifying physiological principle: neighbouring cells join forces to transmit appreciable normal stress across the cell-cell junction, but migrate along orientations of minimal intercellular shear stress.

Real-space imaging of nucleation and growth in colloidal crystallization

Crystallization of concentrated colloidal suspensions was studied in real space with laser scanning confocal microscopy. Direct imaging in three dimensions allowed identification and observation of both nucleation and growth of crystalline regions, providing an experimental measure of properties of the nucleating crystallites. By following their evolution, we identified critical nuclei, determined nucleation rates, and measured the average surface tension of the crystal-liquid interface. The structure of the nuclei was the same as the bulk solid phase, random hexagonal close-packed, and their average shape was rather nonspherical, with rough rather than faceted surfaces.

Geometrically mediated breakup of drops in microfluidic devices

Microfluidic technology offers capabilities for the precise handling of small fluid volumes dispersed as droplets. To fully exploit this potential requires simultaneous generation of multiple size droplets. We demonstrate two methods for passively breaking larger drops into precisely controlled daughter drops using pressure-driven flow in simple microfluidic configurations: (i) a T junction and (ii) flow past isolated obstacles. We quantify conditions for breakup at a T junction and illustrate sequential breakup at T junctions for making small drops at high dispersed phase volume fractions.

Biocompatible surfactants for water-in-fluorocarbon emulsions

Drops of water-in-fluorocarbon emulsions have great potential for compartmentalizing both in vitro and in vivo biological systems; however, surfactants to stabilize such emulsions are scarce. Here we present a novel class of fluorosurfactants that we synthesize by coupling oligomeric perfluorinated polyethers (PFPE) with polyethyleneglycol (PEG). We demonstrate that these block copolymer surfactants stabilize water-in-fluorocarbon oil emulsions during all necessary steps of a drop-based experiment including drop formation, incubation, and reinjection into a second microfluidic device. Furthermore, we show that aqueous drops stabilized with these surfactants can be used for in vitro translation (IVT), as well as encapsulation and incubation of single cells. The compatability of this emulsion system with both biological systems and polydimethylsiloxane (PDMS) microfluidic devices makes these surfactants ideal for a broad range of high-throughput, drop-based applications.

Jamming phase diagram for attractive particles

A wide variety of systems, including granular media, colloidal suspensions and molecular systems, exhibit non-equilibrium transitions from a fluid-like to a solid-like state, characterized solely by the sudden arrest of their dynamics. Crowding or jamming of the constituent particles traps them kinetically, precluding further exploration of the phase space. The disordered fluid-like structure remains essentially unchanged at the transition. The jammed solid can be refluidized by thermalization, through temperature or vibration, or by an applied stress. The generality of the jamming transition led to the proposal of a unifying description, based on a jamming phase diagram. It was further postulated that attractive interactions might have the same effect in jamming the system as a confining pressure, and thus could be incorporated into the generalized description. Here we study experimentally the fluid-to-solid transition of weakly attractive colloidal particles, which undergo markedly similar gelation behaviour with increasing concentration and decreasing thermalization or stress. Our results support the concept of a jamming phase diagram for attractive colloidal particles, providing a unifying link between the glass transition, gelation and aggregation.

Dripping to jetting transitions in coflowing liquid streams

A liquid forced through an orifice into an immiscible fluid ultimately breaks into drops due to surface tension. Drop formation can occur right at the orifice in a dripping process. Alternatively, the inner fluid can form a jet, which breaks into drops further downstream. The transition from dripping to jetting is not understood for coflowing fluid streams, unlike the case of drop formation in air. We show that in a coflowing stream this transition can be characterized by a state diagram that depends on the capillary number of the outer fluid and the Weber number of the inner fluid.

Glass-like dynamics of collective cell migration

Collective cell migration in tissues occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion, yet most detailed knowledge of cell migration comes from single-cell studies. As single cells migrate, the shape of the cell body fluctuates dramatically through cyclic processes of extension, adhesion, and retraction, accompanied by erratic changes in migration direction. Within confluent cell layers, such subcellular motions must be coupled between neighbors, yet the influence of these subcellular motions on collective migration is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously measuring collective migration and subcellular motions, covering a broad range of length scales, time scales, and cell densities. At large length scales and time scales collective migration slows as cell density rises, yet the fastest cells move in large, multicell groups whose scale grows with increasing cell density. This behavior has an intriguing analogy to dynamic heterogeneities found in particulate systems as they become more crowded and approach a glass transition. In addition we find a diminishing self-diffusivity of short-wavelength motions within the cell layer, and growing peaks in the vibrational density of states associated with cooperative cell-shape fluctuations. Both of these observations are also intriguingly reminiscent of a glass transition. Thus, these results provide a broad and suggestive analogy between cell motion within a confluent layer and the dynamics of supercooled colloidal and molecular fluids approaching a glass transition.

Microtubules can bear enhanced compressive loads in living cells because of lateral reinforcement

Cytoskeletal microtubules have been proposed to influence cell shape and mechanics based on their ability to resist large-scale compressive forces exerted by the surrounding contractile cytoskeleton. Consistent with this, cytoplasmic microtubules are often highly curved and appear buckled because of compressive loads. However, the results of in vitro studies suggest that microtubules should buckle at much larger length scales, withstanding only exceedingly small compressive forces. This discrepancy calls into question the structural role of microtubules, and highlights our lack of quantitative knowledge of the magnitude of the forces they experience and can withstand in living cells. We show that intracellular microtubules do bear large-scale compressive loads from a variety of physiological forces, but their buckling wavelength is reduced significantly because of mechanical coupling to the surrounding elastic cytoskeleton. We quantitatively explain this behavior, and show that this coupling dramatically increases the compressive forces that microtubules can sustain, suggesting they can make a more significant structural contribution to the mechanical behavior of the cell than previously thought possible.