Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Particle-Templated Emulsification for Microfluidics-Free Digital Biology.

ABSTRACT: The compartmentalization of reactions in monodispersed droplets is valuable for applications across biology. However, the requirement of microfluidics to partition the sample into monodispersed droplets is a significant barrier that impedes implementation. Here, we introduce particle-templated emulsification, a method to encapsulate samples in monodispersed emulsions without microfluidics. By vortexing a mixture of hydrogel particles and sample solution, we encapsulate the sample in monodispersed emulsions that are useful for most droplet applications. We illustrate the method with ddPCR and single cell culture. The ability to encapsulate samples in monodispersed droplets without microfluidics should facilitate the implementation of compartmentalized reactions in biology.

SUBMITTER: Hatori MN

PROVIDER: S-EPMC6122844 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Particle-Templated Emulsification for Microfluidics-Free Digital Biology.

Hatori Makiko N MN Kim Samuel C SC Abate Adam R AR

Analytical chemistry 20180801 16

The compartmentalization of reactions in monodispersed droplets is valuable for applications across biology. However, the requirement of microfluidics to partition the sample into monodispersed droplets is a significant barrier that impedes implementation. Here, we introduce particle-templated emulsification, a method to encapsulate samples in monodispersed emulsions without microfluidics. By vortexing a mixture of hydrogel particles and sample solution, we encapsulate the sample in monodisperse ...[more]

PMID: 30033717

Similar Datasets

Microfluidics-free single-cell genomics with templated emulsification

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-01-12 | GSE202919 | GEO

Microfluidics-free single-cell genomics with templated emulsification

Project description:Microfluidics-free single-cell genomics with templated emulsification

| PRJNA838959 | ENA

Effect of Flow Rate Modulation on Alginate Emulsification in Multistage Microfluidics.

Project description:The encapsulation of stem cells into alginate microspheres is an important aspect of tissue engineering or bioprinting which ensures cell growth and development. We previously demonstrated the encapsulation of stem cells using the hanging drop method. However, this conventional process takes a relatively long time and only produces a small-volume droplet. Here, an experimental approach for alginate emulsification in multistage microfluidics is reported. By using the microfluidic method, the emulsification of alginate in oil can be manipulated by tuning the flow rate for both phases. Two-step droplet emulsification is conducted in a series of polycarbonate and polydimethylsiloxane microfluidic chips. Multistage emulsification of alginate for stem cell encapsulation has been successfully reported in this study under certain flow rates. Fundamental non-dimensional numbers such as Reynolds and capillary are used to evaluate the effect of flow rate on the emulsification process. Reynolds numbers of around 0.5-2.5 for alginate/water and 0.05-0.2 for oil phases were generated in the current study. The capillary number had a maximum value of 0.018 to ensure the formation of plug flow. By using the multistage emulsification system, the flow rates of each process can be tuned independently, offering a wider range of droplet sizes that can be produced. A final droplet size of 500-1000 µm can be produced using flow rates of 0.1-0.5 mL/h and 0.7-2.4 mL/h for the first stage and second stage, respectively.

| S-EPMC10609249 | biostudies-literature

DIRECT: Digital Microfluidics for Isolation-Free Shared Library Construction of Single-Cell DNA Methylome and Transcriptome

Project description:Integrated single-cell transcriptome and DNA methylome profiling has provided insight into the complex regulatory networks of cells. Existing methods are based on picking a single-cell and performing library construction in a tube, which is costly and cumbersome. Here, we propose DIRECT, a digital microfluidics-based method for simultaneous analysis of the methylome and transcriptome in a single library construction. The accuracy of DIRECT is demonstrated in comparison with bulk and single-omics data, and the high CpG site coverage of DIRECT allows for precise analysis of copy number variation information, enabling expansion of single cell analysis from two- to three-omics. By applying DIRECT to monitor the dynamics of mouse embryonic stem cell differentiation, the relationship between DNA methylation and changes in gene expression during differentiation was revealed. DIRECT enables accurate, robust, and reproducible single-cell DNA methylation and gene expression co-analysis at a lower cost and with greater efficiency, broadening the application scenarios of single-cell multi-omics analysis and revealing a more comprehensive and fine-grained map of cellular regulatory landscapes.

2023-08-10 | GSE240579 | GEO

Particle focusing by 3D inertial microfluidics.

Project description:Three-dimensional (3D) particle focusing in microfluidics is a fundamental capability with a wide range of applications, such as on-chip flow cytometry, where high-throughput analysis at the single-cell level is performed. Currently, 3D focusing is achieved mainly in devices with complex layouts, additional sheath fluids, and complex pumping systems. In this work, we present a compact microfluidic device capable of 3D particle focusing at high flow rates and with a small footprint, without the requirement of external fields or lateral sheath flows, but using only a single-inlet, single-outlet microfluidic sequence of straight channels and tightly curving vertical loops. This device exploits inertial fluidic effects that occur in a laminar regime at sufficiently high flow rates, manipulating the particle positions by the combination of inertial lift forces and Dean drag forces. The device is fabricated by femtosecond laser irradiation followed by chemical etching, which is a simple two-step process enabling the creation of 3D microfluidic networks in fused silica glass substrates. The use of tightly curving three-dimensional microfluidic loops produces strong Dean drag forces along the whole loop but also induces an asymmetric Dean flow decay in the subsequent straight channel, thus producing rapid cross-sectional mixing flows that assist with 3D particle focusing. The use of out-of-plane loops favors a compact parallelization of multiple focusing channels, allowing one to process large amounts of samples. In addition, the low fluidic resistance of the channel network is compatible with vacuum driven flows. The resulting device is quite interesting for high-throughput on-chip flow cytometry.

| S-EPMC6444990 | biostudies-literature

Hydrogel discs for digital microfluidics.

Project description:Hydrogels are networks of hydrophilic polymer chains that are swollen with water, and they are useful for a wide range of applications because they provide stable niches for immobilizing proteins and cells. We report here the marriage of hydrogels with digital microfluidic devices. Until recently, digital microfluidics, a fluid handling technique in which discrete droplets are manipulated electromechanically on the surface of an array of electrodes, has been used only for homogeneous systems involving liquid reagents. Here, we demonstrate for the first time that the cylindrical hydrogel discs can be incorporated into digital microfluidic systems and that these discs can be systematically addressed by droplets of reagents. Droplet movement is observed to be unimpeded by interaction with the gel discs, and gel discs remain stationary when droplets pass through them. Analyte transport into gel discs is observed to be identical to diffusion in cases in which droplets are incubated with gels passively, but transport is enhanced when droplets are continually actuated through the gels. The system is useful for generating integrated enzymatic microreactors and for three-dimensional cell culture. This paper demonstrates a new combination of techniques for lab-on-a-chip systems which we propose will be useful for a wide range of applications.

| S-EPMC3365348 | biostudies-other

Comparative Nanofabrication of PLGA-Chitosan-PEG Systems Employing Microfluidics and Emulsification Solvent Evaporation Techniques.

Project description:Poor circulation stability and inadequate cell membrane penetration are significant impediments in the implementation of nanocarriers as delivery systems for therapeutic agents with low bioavailability. This research discusses the fabrication of a biocompatible poly(lactide-co-glycolide) (PLGA) based nanocarrier with cationic and hydrophilic surface properties provided by natural polymer chitosan and coating polymer polyethylene glycol (PEG) for the entrapment of the hydrophobic drug disulfiram. The traditional emulsification solvent evaporation method was compared to a microfluidics-based method of fabrication, with the optimisation of the parameters for each method, and the PEGylation densities on the experimental nanoparticle formulations were varied. The size and surface properties of the intermediates and products were characterised and compared by dynamic light scattering, scanning electron microscopy and X-ray diffraction, while the thermal properties were investigated using thermogravimetric analysis and differential scanning calorimetry. Results showed optimal particle properties with an intermediate PEG density and a positive surface charge for greater biocompatibility, with nanoparticle surface characteristics shielding physical interaction of the entrapped drug with the exterior. The formulations prepared using the microfluidic method displayed superior surface charge, entrapment and drug release properties. The final system shows potential as a component of a biocompatible nanocarrier for poorly soluble drugs.

| S-EPMC7564778 | biostudies-literature

Droplet-based pyrosequencing using digital microfluidics.

Project description:The feasibility of implementing pyrosequencing chemistry within droplets using electrowetting-based digital microfluidics is reported. An array of electrodes patterned on a printed-circuit board was used to control the formation, transportation, merging, mixing, and splitting of submicroliter-sized droplets contained within an oil-filled chamber. A three-enzyme pyrosequencing protocol was implemented in which individual droplets contained enzymes, deoxyribonucleotide triphosphates (dNTPs), and DNA templates. The DNA templates were anchored to magnetic beads which enabled them to be thoroughly washed between nucleotide additions. Reagents and protocols were optimized to maximize signal over background, linearity of response, cycle efficiency, and wash efficiency. As an initial demonstration of feasibility, a portion of a 229 bp Candida parapsilosis template was sequenced using both a de novo protocol and a resequencing protocol. The resequencing protocol generated over 60 bp of sequence with 100% sequence accuracy based on raw pyrogram levels. Excellent linearity was observed for all of the homopolymers (two, three, or four nucleotides) contained in the C. parapsilosis sequence. With improvements in microfluidic design it is expected that longer reads, higher throughput, and improved process integration (i.e., "sample-to-sequence" capability) could eventually be achieved using this low-cost platform.

| S-EPMC3690483 | biostudies-literature

Laser particle activated cell sorting in microfluidics.

Project description:Laser particles providing bright, spectrally narrowband emission renders them suitable for use as cellular barcodes. Here, we demonstrate a microfluidic platform integrated with a high-speed spectrometer, capable of reading the emission from laser particles in fluidic channels and routing cells based on their optical barcodes. The sub-nanometer spectral emission of each laser particle enables us to distinguish individual cells labeled with hundreds of different laser colors in the near infrared. Furthermore, cells tagged with laser particles are sorted based on their spectral barcodes at a kilohertz rate by using a real-time field programmable gate array and 2-way electric field switch. We demonstrate several different flavors of sorting, including isolation of barcoded cells, and cells tagged with a specific laser color. We term this novel sorting technique laser particle activated cell sorting (LACS). This flow reading and sorting technology adds to the arsenal of single-cell analysis tools using laser particles.

| S-EPMC9195882 | biostudies-literature

Digital Microfluidics for Nucleic Acid Amplification.

Project description:Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

| S-EPMC5539496 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data