Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Controller for microfluidic large-scale integration.

ABSTRACT: Microfluidic devices with integrated valves provide precise, programmable fluid handling platforms for high-throughput biological or chemical assays. However, setting up the infrastructure to control such platforms often requires specific engineering expertise or expensive commercial solutions. To address these obstacles, we present a Kit for Arduino-based Transistor Array Actuation (KATARA), an open-source and low-cost Arduino-based controller that can drive 70 solenoid valves to pneumatically actuate integrated microfluidic valves. We include a python package with a GUI to control the KATARA from a personal computer. No programming experience is required.

SUBMITTER: White JA

PROVIDER: S-EPMC6373447 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Controller for microfluidic large-scale integration.

White Jonathan A JA Streets Aaron M AM

HardwareX 20171031

Microfluidic devices with integrated valves provide precise, programmable fluid handling platforms for high-throughput biological or chemical assays. However, setting up the infrastructure to control such platforms often requires specific engineering expertise or expensive commercial solutions. To address these obstacles, we present a Kit for Arduino-based Transistor Array Actuation (KATARA), an open-source and low-cost Arduino-based controller that can drive 70 solenoid valves to pneumatically ...[more]

PMID: 30775638

Similar Datasets

Large-Scale Integration of All-Glass Valves on a Microfluidic Device.

Project description:In this study, we developed a method for fabricating a microfluidic device with integrated large-scale all-glass valves and constructed an actuator system to control each of the valves on the device. Such a microfluidic device has advantages that allow its use in various fields, including physical, chemical, and biochemical analyses and syntheses. However, it is inefficient and difficult to integrate the large-scale all-glass valves in a microfluidic device using conventional glass fabrication methods, especially for the through-hole fabrication step. Therefore, we have developed a fabrication method for the large-scale integration of all-glass valves in a microfluidic device that contains 110 individually controllable diaphragm valve units on a 30 mm × 70 mm glass slide. This prototype device was fabricated by first sandwiching a 0.4-mm-thick glass slide that contained 110 1.5-mm-diameter shallow chambers, each with two 50-?m-diameter through-holes, between an ultra-thin glass sheet (4 ?m thick) and another 0.7-mm-thick glass slide that contained etched channels. After the fusion bonding of these three layers, the large-scale microfluidic device was obtained with integrated all-glass valves consisting of 110 individual diaphragm valve units. We demonstrated its use as a pump capable of generating a flow rate of approximately 0.06?5.33 ?L/min. The maximum frequency of flow switching was approximately 12 Hz.

| S-EPMC6190260 | biostudies-literature

Silicon and glass very large scale microfluidic droplet integration for terascale generation of polymer microparticles.

Project description:Microfluidic chips can generate emulsions, which can be used to synthesize polymer microparticles that have superior pharmacological performance compared to particles prepared by conventional techniques. However, low production rates of microfluidics remains a challenge to successfully translate laboratory discoveries to commercial manufacturing. We present a silicon and glass device that incorporates an array of 10,260 (285?×?36) microfluidic droplet generators that uses only a single set of inlets and outlets, increasing throughput by >10,000× compared to microfluidics with a single generator. Our design breaks the tradeoff between the number of generators and the maximum throughput of individual generators by incorporating high aspect ratio flow resistors. We test these design strategies by generating hexadecane microdroplets at >1 trillion droplets per h with a coefficient of variation CV <3%. To demonstrate the synthesis of biocompatible microparticles, we generated 8-16?µm polycaprolactone particles with a CV <5% at a rate of 277?g?h-1.

| S-EPMC5964316 | biostudies-literature

Detailing regulatory networks through large scale data integration.

Project description:MotivationMuch of a cell's regulatory response to changing environments occurs at the transcriptional level. Particularly in higher organisms, transcription factors (TFs), microRNAs and epigenetic modifications can combine to form a complex regulatory network. Part of this system can be modeled as a collection of regulatory modules: co-regulated genes, the conditions under which they are co-regulated and sequence-level regulatory motifs.ResultsWe present the Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction (COALESCE) system for regulatory module prediction. The algorithm is efficient enough to discover expression biclusters and putative regulatory motifs in metazoan genomes (>20,000 genes) and very large microarray compendia (>10,000 conditions). Using Bayesian data integration, it can also include diverse supporting data types such as evolutionary conservation or nucleosome placement. We validate its performance using a functional evaluation of co-clustered genes, known yeast and Escherichea coli TF targets, synthetic data and various metazoan data compendia. In all cases, COALESCE performs as well or better than current biclustering and motif prediction tools, with high accuracy in functional and TF/target assignments and zero false positives on synthetic data. COALESCE provides an efficient and flexible platform within which large, diverse data collections can be integrated to predict metazoan regulatory networks.AvailabilitySource code (C++) is available at http://function.princeton.edu/sleipnir, and supporting data and a web interface are provided at http://function.princeton.edu/coalesce.Contactogt@cs.princeton.edu; hcoller@princeton.edu.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC2788929 | biostudies-literature

Large-scale integration of human genetic and physical maps.

Project description:Genetic maps are used routinely in family-based linkage studies to identify the rough location of genes that influence human traits and diseases. Unlike physical maps, genetic maps are based on the amount of recombination occurring between adjacent loci rather than the actual number of bases separating them. Genetic maps are constructed by statistically characterizing the number of crossovers observed in parental meioses leading to the transmission of alleles to their offspring. Considerations such as the number of meioses observed, the heterozygosity and physical distance between the loci studied, and the statistical methods used can impact the construction and reliability of a genetic map. As is well known, poorly constructed genetic maps can have adverse effects on linkage mapping studies. With the availability of sequence-based maps, as well as genetic maps generated by different researchers (such as those generated by the Marshfield and deCODE groups), one can investigate the compatibility and properties of different maps. We have integrated information from the most current human genome sequence data (UCSC genome assembly Human July 2003) as well as 8399 microsatellite markers used in the Marshfield and deCODE maps to reconcile the these maps. Our efforts resulted in updated sex-specific genetic maps.

| S-EPMC419799 | biostudies-literature

Large-scale microbiome data integration enables robust biomarker identification.

Project description:The close association between gut microbiota dysbiosis and human diseases is being increasingly recognized. However, contradictory results are frequently reported, as confounding effects exist. The lack of unbiased data integration methods is also impeding the discovery of disease-associated microbial biomarkers from different cohorts. Here we propose an algorithm, NetMoss, for assessing shifts of microbial network modules to identify robust biomarkers associated with various diseases. Compared to previous approaches, the NetMoss method shows better performance in removing batch effects. Through comprehensive evaluations on both simulated and real datasets, we demonstrate that NetMoss has great advantages in the identification of disease-related biomarkers. Based on analysis of pandisease microbiota studies, there is a high prevalence of multidisease-related bacteria in global populations. We believe that large-scale data integration will help in understanding the role of the microbiome from a more comprehensive perspective and that accurate biomarker identification will greatly promote microbiome-based medical diagnosis.

| S-EPMC10766547 | biostudies-literature

A microfluidic array for large-scale ordering and orientation of embryos.

Project description:Quantitative studies of embryogenesis require the ability to monitor pattern formation and morphogenesis in large numbers of embryos, at multiple time points and in diverse genetic backgrounds. We describe a simple approach that greatly facilitates these tasks for Drosophila melanogaster embryos, one of the most advanced models of developmental genetics. Based on passive hydrodynamics, we developed a microfluidic embryo-trap array that can be used to rapidly order and vertically orient hundreds of embryos. We describe the physical principles of the design and used this platform to quantitatively analyze multiple morphogen gradients in the dorsoventral patterning system. Our approach can also be used for live imaging and, with slight modifications, could be adapted for studies of pattern formation and morphogenesis in other model organisms.

| S-EPMC4100329 | biostudies-literature

Large-Scale Preparation of Hair Follicle Germs Using a Microfluidic Device.

Project description:Hair follicle morphogenesis during embryonic development is driven by the formation of hair follicle germs (HFGs) via interactions between epithelial and mesenchymal cells. Bioengineered HFGs are potential tissue grafts for hair regenerative medicine because they can replicate interactions and hair follicle morphogenesis after transplantation. However, a mass preparation approach for HFGs is necessary for clinical applications, given that thousands of de novo hair follicles are required to improve the appearance of a single patient with alopecia. In this study, we developed a microfluidics-based approach for the large-scale preparation of HFGs. A simple flow-focusing microfluidic device allowed collagen solutions containing epithelial and mesenchymal cells to flow and generate collagen microbeads with distinct Janus structures. During the 3 days of culture, the collagen beads contracted owing to cellular traction forces, resulting in collagen- and cell-dense HFGs. The transplantation of HFGs into nude mice resulted in highly efficient de novo hair follicle regeneration. This method provides a scalable and robust tissue graft preparation approach for hair regeneration.

| S-EPMC10865290 | biostudies-literature

Large-scale integration of nanoelectromechanical systems for gas sensing applications.

Project description:We have developed arrays of nanomechanical systems (NEMS) by large-scale integration, comprising thousands of individual nanoresonators with densities of up to 6 million NEMS per square centimeter. The individual NEMS devices are electrically coupled using a combined series-parallel configuration that is extremely robust with respect to lithographical defects and mechanical or electrostatic-discharge damage. Given the large number of connected nanoresonators, the arrays are able to handle extremely high input powers (>1 W per array, corresponding to <1 mW per nanoresonator) without excessive heating or deterioration of resonance response. We demonstrate the utility of integrated NEMS arrays as high-performance chemical vapor sensors, detecting a part-per-billion concentration of a chemical warfare simulant within only a 2 s exposure period.

| S-EPMC3839335 | biostudies-literature

Large-scale, heterogeneous integration of nanowire arrays for image sensor circuitry.

Project description:We report large-scale integration of nanowires for heterogeneous, multifunctional circuitry that utilizes both the sensory and electronic functionalities of single crystalline nanomaterials. Highly ordered and parallel arrays of optically active CdSe nanowires and high-mobility Ge/Si nanowires are deterministically positioned on substrates, and configured as photodiodes and transistors, respectively. The nanowire sensors and electronic devices are then interfaced to enable an all-nanowire circuitry with on-chip integration, capable of detecting and amplifying an optical signal with high sensitivity and precision. Notably, the process is highly reproducible and scalable with a yield of approximately 80% functional circuits, therefore, enabling the fabrication of large arrays (i.e., 13 x 20) of nanowire photosensor circuitry with image-sensing functionality. The ability to interface nanowire sensors with integrated electronics on large scales and with high uniformity presents an important advance toward the integration of nanomaterials for sensor applications.

| S-EPMC2516247 | biostudies-other

Large-scale analysis of the integration of enhancer-enhancer signals by promoters

Project description:Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities are combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it is not clear which of these modes are more frequent in mammalian genomes. Here, we systematically tested how pairs of enhancers activate promoters using a three-way combinatorial reporter assay in mouse cells. By assaying about 69,000 enhancer-enhancer-promoter combinations we found that enhancer pairs generally combine near-additively. This behaviour was conserved across seven developmental promoters tested. Surprisingly, these promoters scale the enhancer signals approximately following a power-law, but the exponent of this response varies between promoters. A housekeeping promoter showed an overall different response to enhancer pairs, and a smaller dynamic range. Thus, our data indicate that enhancers mostly act additively, but promoters transform their collective effect non-linearly.

2023-08-10 | GSE240586 | GEO

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