spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content

CRISPR Digital Sensing: From Micronano-Collaborative Chip to Biomolecular Detection

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) sensing technology proved to be valuable during the COVID-19 pandemic through its sensitivity, specificity, robustness, and versatility. However, issues such as overreliance on amplification, susceptibility to false positives, lack of quantification strategies, and complex operation procedures have hindered its broader application in bioanalysis and clinical diagnostics. The collision between micronano-collaborative chips and CRISPR technology has effectively addressed these bottlenecks, offering innovative solutions for diagnosis and treatment. Unlike conventional micronano chips, micronano digital chips enhance CRISPR's response to trace amounts of target molecules by leveraging highly controllable local environments and compartmentalized microreactors. This advancement improves detection efficiency and revolutionizes traditional in vitro bioanalytical processes. First, the working principles, fabrication techniques, and performance metrics of CRISPR-based digital droplet microfluidics and microarray chips are examined. Then, the applications of CRISPR digital sensing chips in bioassays are reviewed, emphasizing their importance in advancing in vitro detection systems for gene editing. Finally, the prospects of CRISPR digital sensing technology are explored, particularly its potential for body surface biomonitoring and its broader development opportunities in the biomedical field.

Cap-Drop: A Pre-Programmed, Self-Powered Capillary Microfluidic System for Passive Droplet Generation and 3D Cell Culture Modeling

3D cell culture models and precision diagnostics have advanced significantly through microfluidic systems, yet their broad implementation remains limited by challenges in scalability, integration, and portability. Effective 3D cell culture models require systems that maintain sample integrity, minimize evaporation, and avoid crosstalk while handling various biofluids. However, current platforms often depend on active pumping, bulky components, and complex controls, which hinder portability, usability, and affordability. To address these challenges, the Capillary Droplet microfluidic (Cap-Drop) is presented, a novel capillary-driven platform that generates and immobilizes droplets with precision, eliminating the need for external pumps or intricate setups. Unlike conventional system, where moving droplets complicate tracking and identification, Cap-Drop ensures fixed droplet positioning, allowing seamless tracking and analysis. By integrating hydrophilic and hydrophobic materials with several innovative capillary elements -including passive vents (PV), pressure reducer (PR), stop valves (SV), delay channels, and bubble trap (BT)-Cap-Drop enables robust droplet formation (40 to 500 nL) for biofluids of varying properties. The pre-programmed design of PV in corporation with other capillary elements autonomously seals microwells (MWs), ensuring consistent sample digitization and supress risk of evaporation. Cap-Drop is optimized and offers a transformative platform for microfluidic technologies in mechanistic cellular studies, preclinical drug screening, and clinical diagnostics.

Advanced droplet microfluidic platform for high-throughput screening of industrial fungi

Industrial fungi are pivotal candidates for the production of a diverse array of bioproducts. To enhance their productivity, these strains are frequently subjected to genetic modifications. Following transformation, the selection of optimal production strains is critical; however, traditional screening methods often suffer from limitations in throughput and sensitivity. This article explores the transformative potential of Droplet Microfluidic Technology (DMFS) for high-throughput screening of industrial fungi. DMFS enables real-time monitoring and precise single-cell analysis by encapsulating individual fungal spores or cells within droplets, ranging from picoliters to nanoliters, functioning as isolated microreactors. This technology effectively addresses the challenges posed by conventional methods, such as agar plate assays and fluorescence-activated cell sorting. Key advancements discussed include microfluidic chip fabrication, droplet generation and regulation techniques, and multimodal signal detection methods-encompassing fluorescence, Raman spectroscopy, and mass spectrometry. Notably, strategies to mitigate droplet breakage in filamentous fungi, including physical constraints, bionic core-shell hydrogels, and genetic engineering approaches, are analyzed to prolong stable culture times. Future developments will likely emphasize interdisciplinary applications, including automation driven by artificial intelligence and label-free detection methods. We anticipate that this review will catalyze further research into high-quality industrial fungi, thereby promoting sustainable biomanufacturing through enhanced throughput, cost-effectiveness, and scalability.

Gray-Level Guided Image-Activated Droplet Sorter for Label-Free, High-Accuracy Screening of Single-Cell on Demand

Single-cell encapsulation in droplet microfluidics has become a powerful tool in precision medicine, single-cell analysis, and immunotherapy. However, droplet generation with a single-cell encapsulation is a random process, which also results in a large number of empty and multi-cell droplets. Current microfluidics sorting technologies suffer from drawbacks such as fluorescent labeling, inability to remove multi-cell droplets, or low throughput. This paper presents a gray-level guided image-activated droplet sorter (GL-IADS), which enables label-free, high-accuracy screening of single-cell droplets by rejecting empty and multi-cell droplets. The gray-level based recognition method can accurately classify droplet images (empty, single-cell, and multi-cell droplets), especially in differentiating empty and cell-laden droplets (accuracy of 100%). Crucially, this method reduces the image processing time to ≈300 µs, which makes the GL-IADS possible to reach an ultra-high sorting throughput up to hundreds or even KHz. The GL-IADS integrates the novel recognition method with a detachable acoustofluidic system, achieving sorting purity of 97.9%, 97.4%, and >99% for single-cell, multi-cell, and cell-laden droplets, respectively, with a throughput of 43 Hz. The GL-IADS holds promise for numerous biological applications that are previously difficult with fluorescence-based technologies.

An acoustofluidic embedding platform for rapid multiphase microparticle injection

Droplet manipulation technologies play a critical role in many aspects of biochemical research, including in complex reaction assays useful for drug delivery, for building artificial cells, and in synthetic biology. While advancements have been made in manipulating liquid droplets, the capability to freely and dynamically manipulate solid objects across aqueous and oil phases remains unexplored. Here, we develop an acoustofluidic frequency-associated microsphere embedding platform, which enables microscale rapid injection of microparticles from a fluorinated oil into aqueous droplets. By observing different embedding mechanisms at low and high acoustic frequencies, we establish a theoretical model and practical principles for cross-phase manipulations. The proposed system not only enables multi-phase manipulation but also provides contactless control of specific microparticles within various distinctive phases. We demonstrate the acoustic-driven embedding and subsequent on-demand disassembly of hydrogel microspheres. This system indicates potential for reagent delivery and molecule capture applications. It enhances existing droplet manipulation technologies by enabling both multi-phase and cross-phase operations, paving the way for solid-liquid interaction studies in artificial cell research. The capability for intricate multi-phase loading, transport, and reactions offers promising implications for various fields, including in-droplet biochemical assays, drug delivery, and synthetic biology.

Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research

In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies have established themselves as key tools for dissecting genetic sequences at the level of single cells. These technologies reveal cellular diversity and allow for the exploration of cell states and transformations with exceptional resolution. Unlike bulk sequencing, which provides population-averaged data, scRNA-seq can detect cell subtypes or gene expression variations that would otherwise be overlooked. However, a key limitation of scRNA-seq is its inability to preserve spatial information about the RNA transcriptome, as the process requires tissue dissociation and cell isolation. Spatial transcriptomics is a pivotal advancement in medical biotechnology, facilitating the identification of molecules such as RNA in their original spatial context within tissue sections at the single-cell level. This capability offers a substantial advantage over traditional single-cell sequencing techniques. Spatial transcriptomics offers valuable insights into a wide range of biomedical fields, including neurology, embryology, cancer research, immunology, and histology. This review highlights single-cell sequencing approaches, recent technological developments, associated challenges, various techniques for expression data analysis, and their applications in disciplines such as cancer research, microbiology, neuroscience, reproductive biology, and immunology. It highlights the critical role of single-cell sequencing tools in characterizing the dynamic nature of individual cells.

inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples

The expansion of single-cell analytical techniques has empowered the exploration of diverse biological questions at the individual cells. Droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly widely used due to their high-throughput capabilities and small reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, their relatively high cost limits the ability to profile large numbers of cells and samples. Moreover, as the scale of single-cell sequencing continues to expand, accommodating diverse workflows and cost-effective multi-biospecimen profiling becomes more critical. Herein, we present inDrops-2, an open-source scRNA-seq technology designed to profile live or preserved cells with a sensitivity matching that of state-of-the-art commercial systems but at a 6-fold lower cost. We demonstrate the flexibility of inDrops-2, by implementing two prominent scRNA-seq protocols, based on exponential and linear amplification of barcoded-complementary DNA, and provide useful insights into the advantages and disadvantages inherent to each approach. We applied inDrops-2 to simultaneously profile multiple human lung carcinoma samples that had been subjected to cell preservation, long-term storage and multiplexing to obtain a multiregional cellular profile of the tumor microenvironment. The scalability, sensitivity and cost efficiency make inDrops-2 stand out among other droplet-based scRNA-seq methods, ideal for large-scale studies on rare cell molecular signatures.

scTrends: A living review of commercial single-cell and spatial 'omic technologies

Understanding the rapidly evolving landscape of single-cell and spatial omic technologies is crucial for advancing biomedical research and drug development. We provide a living review of both mature and emerging commercial platforms, highlighting key methodologies and trends shaping the field. This review spans from foundational single-cell technologies such as microfluidics and plate-based methods to newer approaches like combinatorial indexing; on the spatial side, we consider next-generation sequencing and imaging-based spatial transcriptomics. Finally, we highlight emerging methodologies that may fundamentally expand the scope for data generation within pharmaceutical research, creating opportunities to discover and validate novel drug mechanisms. Overall, this review serves as a critical resource for navigating the commercialization and application of single-cell and spatial omic technologies in pharmaceutical and academic research.

Droplet-based single-cell sequencing: Strategies and applications

Notable advancements in single-cell omics technologies have not only addressed longstanding challenges but also enabled unprecedented studies of cellular heterogeneity with unprecedented resolution and scale. These strides have led to groundbreaking insights into complex biological systems, paving the way for a more profound comprehension of human biology and diseases. The droplet microfluidic technology has become a crucial component in many single-cell sequencing workflows in terms of throughput, cost-effectiveness, and automation. Utilizing a microfluidic chip to encapsulate and profile individual cells within droplets has significantly improved single-cell research. Therefore, this review aims to comprehensively elaborate the droplet microfluidics-assisted omics methods from a single-cell perspective. The strategies for using droplet microfluidics in the realms of genomics, epigenomics, transcriptomics, and proteomics analyses are first introduced. On this basis, the focus then turns to the latest applications of this technology in different sequencing patterns, including mono- and multi-omics. Finally, the challenges and further perspectives of droplet-based single-cell sequencing in both foundational research and commercial applications are discussed.

An Acoustofluidic Picoinjector

Droplet microfluidics has emerged as a valuable technology for a multitude of chemical and biomedical applications, offering the capability to create independent microenvironments for high-throughput assays. Central to numerous droplet microfluidic applications is the picoinjection of materials into individual droplets, yet existing picoinjection methods often exhibit high power requirements, lack biocompatibility, and/or suffer from limited controllability. Here, we present an acoustofluidic picoinjector that generates acoustic pressure at the droplet interface to enable on-demand, energy-efficient, and biocompatible injection at high precision. We validate our platform by performing acid-base titrations by iteratively injecting picoliter volume reagents into droplets to induce pH transitions detectable by color change in solution. Additionally, we demonstrate the versatility of the acoustofluidic picoinjector in the synthesis of metallic nanoparticles, yielding highly monodisperse and reproducible particle morphologies compared to conventional bulk-phase techniques. By facilitating controlled delivery of reagents or biological samples with unparalleled accuracy, acoustofluidic picoinjection broadens the utility of droplet microfluidics for a myriad of applications in chemical and biological research.

Microfluidic programmable strategies for channels and flow

This review summarizes programmable microfluidics, an advanced method for precise fluid control in microfluidic technology through microchannel design or liquid properties, referring to microvalves, micropumps, digital microfluidics, multiplexers, micromixers, slip-, and block-based configurations. Different microvalve types, including electrokinetic, hydraulic/pneumatic, pinch, phase-change and check valves, cater to diverse experimental needs. Programmable micropumps, such as passive and active micropumps, play a crucial role in achieving precise fluid control and automation. Due to their small size and high integration, microvalves and micropumps are widely used in medical devices and biological analysis. In addition, this review provides an in-depth exploration of the applications of digital microfluidics, multiplexed microfluidics, and mixer-based microfluidics in the manipulation of liquid movement, mixing, and splitting. These methodologies leverage the physical properties of liquids, such as capillary forces and dielectric forces, to achieve precise control over fluid dynamics. SlipChip technology, which branches into rotational SlipChip and translational SlipChip, controls fluid through sliding motion of the microchannel. On the other hand, innovative designs in microfluidic systems pursue better modularity, reconfigurability and ease of assembly. Different assembly strategies, from one-dimensional assembly blocks and two-dimensional Lego®-style blocks to three-dimensional reconfigurable modules, aim to enhance flexibility and accessibility. These technologies enhance user-friendliness and accessibility by offering integrated control systems, making them potentially usable outside of specialized technical labs. Microfluidic programmable strategies for channels and flow hold promising applications in biomedical research, chemical analysis and drug screening, providing theoretical and practical guidance for broader utilization in scientific research and practical applications.

DropBlot: single-cell western blotting of chemically fixed cancer cells

Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.

CellRank 2: unified fate mapping in multiview single-cell data

Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories; however, trajectory inference does not incorporate valuable time point information or utilize additional modalities, whereas methods that address these different data views cannot be combined or do not scale. Here we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of cells in a unified fashion. CellRank 2 consistently recovers terminal states and fate probabilities across data modalities in human hematopoiesis and endodermal development. Our framework also allows combining transitions within and across experimental time points, a feature we use to recover genes promoting medullary thymic epithelial cell formation during pharyngeal endoderm development. Moreover, we enable estimating cell-specific transcription and degradation rates from metabolic-labeling data, which we apply to an intestinal organoid system to delineate differentiation trajectories and pinpoint regulatory strategies.

The Droplet Creeping-Sliding Dynamic Wetting Mechanism on Bionic Self-Cleaning Surfaces

The dynamic wetting behavior of droplets has been of wide concern due to the hazards of accretion/icing of supercooled droplets on engineering components/systems served in low temperature freezing rain environment; thus, it is urgent to establish the relationship between droplet depinning/removing behaviors and surface characteristics. In this article, the actual rotation conditions of moving components such as wind turbine blades are simulated. The self-cleaning hydrophobic coating surface(S1) and bionic superhydrophobic coating surface(S2) show outstanding droplet removal performance compared to hydrophilic bare steel surface(S0), and the average speed of the droplet removal is increased by 400-500%. The "creeping-sliding" behavior of droplets on self-cleaning coatings is investigated by the change of droplet displacement(ΔD). The effect of the energy storage caused by the droplet creeping process provides initial kinetic energy for the droplet removal. Combined with the experimental data and theoretical model, the critical depinning resistance is calculated. The difference of the wetting interface free energy(ΔEx) during the dynamic wetting process of the droplets on the bionic superhydrophobic self-cleaning surface is researched. And the influence mechanism of the droplet embedded depth(x) on the creeping/sliding behavior in the nanotexture is clarified. Thus, the mechanical criterion of droplet depinning is proposed (the error is about 10%). The results can provide a theoretical basis for the design principle of antifreezing rain coatings on moving components.

Image-activated pico-injection for single-cell analysis

The addition of reagents into preformed droplets is a crucial yet intricate task in droplet-based applications where sequential reactions is required. Pico-injection offers high throughput and robustness in accomplishing this task, but the existing pico-injection techniques work in an indiscriminate manner, making it difficult to target particular groups of droplets. Here we report image-activated pico-injection (imgPico) for label-free, on-demand reagent supplementation into droplets. The imgPico detects the droplets of interest by real-time image analysis and makes decisions for the downstream pico-injection operation. We studied the performance of different algorithms for the image analysis and optimized the experimental settings of the imgPico. In the validation experiment, the imgPico successfully injected fluorescent dyes into droplets encapsulating one, two, and three cells, respectively, as expected. We further demonstrated the utility of imgPico by targeting droplets encapsulating single cells in droplet-based single-cell RNA sequencing (scRNA-seq) using exceedingly high cell density, and the results showed that the imgPico effectively reduced the presence of doublets in the scRNA-seq data. With the merits of being label-free and versatile, the imgPico represents a technical advance with potential applications in single-cell analysis.

Advanced sequencing-based high-throughput and long-read single-cell transcriptome analysis

Cells are the fundamental building blocks of living systems, exhibiting significant heterogeneity. The transcriptome connects the cellular genotype and phenotype, and profiling single-cell transcriptomes is critical for uncovering distinct cell types, states, and the interplay between cells in development, health, and disease. Nevertheless, single-cell transcriptome analysis faces daunting challenges due to the low abundance and diverse nature of RNAs in individual cells, as well as their heterogeneous expression. The advent and continuous advancements of next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies have solved these problems and facilitated the high-throughput, sensitive, full-length, and rapid profiling of single-cell RNAs. In this review, we provide a broad introduction to current methodologies for single-cell transcriptome sequencing. First, state-of-the-art advancements in high-throughput and full-length single-cell RNA sequencing (scRNA-seq) platforms using NGS are reviewed. Next, TGS-based long-read scRNA-seq methods are summarized. Finally, a brief conclusion and perspectives for comprehensive single-cell transcriptome analysis are discussed.

Efficient Separation of Methanol Single-Micron Droplets by Tailing Phenomenon Using a PDMS Microfluidic Device

Microdroplet-based fluidic systems have the advantages of small size, short diffusion time, and no cross-contamination; consequently, droplets often provide a fast and precise reaction environment as well as an analytical environment for individual molecules. In order to handle diverse reactions, we developed a method to create organic single-micron droplets (S-MDs) smaller than 5 μm in diameter dispersed in silicone oil without surfactant. The S-MD generation microflow device consists of a mother droplet (MoD) generator and a tapered separation channel featuring multiple side channels. The tapered channel enhanced the shear forces to form tails from the MoDs, causing them to break up. Surface treatment with the fluoropolymer CYTOP protected PDMS fluid devices from organic fluids. The tailing separation of methanol droplets was accomplished without the use of surfactants. The generation of tiny organic droplets may offer new insights into chemical separation and help study the scaling effects of various chemical reactions.

SeParate: multiway fluorescence-activated droplet sorting based on integration of serial and parallel triaging concepts

Fluorescence-activated droplet sorting (FADS) has emerged as a versatile high-throughput sorting tool that is, unlike most fluorescence-activated cell sorting (FACS) platforms, capable of sorting droplet-compartmentalized cells, cell secretions, entire enzymatic reactions and more. Recently, multiplex FADS platforms have been developed for the sorting of multi-fluorophore populations towards different outlets in addition to the standard, more commonly used, 2-way FADS platform. These multiplex FADS platforms consist of either multiple 2-way junctions one after the other (i.e. serial sorters) or of one junction sorting droplets in more than 2 outlets (i.e. parallel sorters). In this work, we present SeParate, a novel platform based on integrating s̲e̲rial and p̲a̲r̲allel sorting principles for accura̲t̲e̲ multiplex droplet sorting that is able to mitigate limitations of current multiplex sorters. We show the SeParate platform and its capability in highly accurate 4-way sorting of a multi-fluorophore population into four subpopulations with the potential to expand to more. More specifically, the SeParate platform was thoroughly validated using mixed populations of fluorescent beads and picoinjected droplets, yielding sorting accuracies up to 100% and 99.9%, respectively. Finally, transfected HEK-293T cells were sorted employing two different optical setups, resulting in an accuracy up to 99.5%. SeParate's high accuracy for a diverse set of samples, including highly variable biological specimens, together with its scalability beyond the demonstrated 4-way sorting, warrants a broad applicability for multi-fluorophore studies in life sciences, environmental sciences and others.

Development and future of droplet microfluidics

Over the past two decades, advances in droplet-based microfluidics have facilitated new approaches to process and analyze samples with unprecedented levels of precision and throughput. A wide variety of applications has been inspired across multiple disciplines ranging from materials science to biology. Understanding the dynamics of droplets enables optimization of microfluidic operations and design of new techniques tailored to emerging demands. In this review, we discuss the underlying physics behind high-throughput generation and manipulation of droplets. We also summarize the applications in droplet-derived materials and droplet-based lab-on-a-chip biotechnology. In addition, we offer perspectives on future directions to realize wider use of droplet microfluidics in industrial production and biomedical analyses.

Antibodies, repertoires and microdevices in antibody discovery and characterization

Therapeutic antibodies are paramount in treating a wide range of diseases, particularly in auto-immunity, inflammation and cancer, and novel antibody candidates recognizing a vast array of novel antigens are needed to expand the usefulness and applications of these powerful molecules. Microdevices play an essential role in this challenging endeavor at various stages since many general requirements of the overall process overlap nicely with the general advantages of microfluidics. Therefore, microfluidic devices are rapidly taking over various steps in the process of new candidate isolation, such as antibody characterization and discovery workflows. Such technologies can allow for vast improvements in time-lines and incorporate conservative antibody stability and characterization assays, but most prominently screenings and functional characterization within integrated workflows due to high throughput and standardized workflows. First, we aim to provide an overview of the challenges of developing new therapeutic candidates, their repertoires and requirements. Afterward, this review focuses on the discovery of antibodies using microfluidic systems, technological aspects of micro devices and small-scale antibody protein characterization and selection, as well as their integration and implementation into antibody discovery workflows. We close with future developments in microfluidic detection and antibody isolation principles and the field in general.