Droplet microfluidics has become a powerful analytical platform in biological research for conducting high-throughput screening in millions of discrete micro-reactors per hour. While the method facilitates faster and cheaper testing than conventional microtiter plates, the mobile nature of droplets makes micro-reaction tracking a notable challenge. To address this, researchers are developing a variety of tracking methods, ranging from organizing droplets into an index or labeling droplets with a barcode. The optimal tracking approach depends on the criteria for each specific application. Considerations include the requisite assay readout, throughput, droplet library size, reagent tracking and more. In this review, we summarize different strategies for droplet micro-reaction tracking and comment on promising future approaches in droplet barcoding. Topics range from indexing droplets by sequence or in an array, labeling droplets with barcodes, and reagent barcoding to track the input conditions in parametric screens.
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http://dx.doi.org/10.1016/j.copbio.2019.05.004 | DOI Listing |
Commun Biol
January 2025
Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Single-cell transcriptomics, which utilises barcodes and unique molecular identifiers (UMIs) for polyA+ mRNA capture, is compromised by oligonucleotide synthesis errors. To address this, we modified the oligonucleotide capture design and integrated an interposed anchor between the barcode and the UMI. This design significantly reduces the need to discard reads due to synthesis inaccuracies.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
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.
View Article and Find Full Text PDFLab Chip
January 2025
Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
Revealing how individual cells alter their secretions over time is crucial for understanding their responses to environmental changes. Key questions include: When do cells modify their functions and states? What transitions occur? Insights into the kinetic secretion trajectories of various cell types are essential for unraveling complex biological systems. This review highlights seven microfluidic technologies for time-resolved single-cell secretion analysis: 1.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Adv Sci (Weinh)
December 2024
Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
Digital PCR (dPCR) has transformed nucleic acid diagnostics by enabling the absolute quantification of rare mutations and target sequences. However, traditional dPCR detection methods, such as those involving flow cytometry and fluorescence imaging, may face challenges due to high costs, complexity, limited accuracy, and slow processing speeds. In this study, SAM-dPCR is introduced, a training-free open-source bioanalysis paradigm that offers swift and precise absolute quantification of biological samples.
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