Digital microfluidic isolation of single cells for -Omics

Lamanna, Julian; Scott, Elaine P.; Edwards, Harrison; Chamberlain, M. Dean; Dryden, Michael D. M.; Peng, Jiaxi; Mair, Barbara; Lee, Adam; Chan, Calvin; Sklavounos, Alexandros; Heffernan, Austin; Abbas, Farhana; Lam, Charis; Olson, Maxwell E.; Moffat, Jason; Wheeler, Aaron R.

doi:10.1038/s41467-020-19394-5

Cited by 90 publications

(76 citation statements)

References 71 publications

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“…To evaluate the background of the single-cell measurement, blank control samples (cell-free supernatant without trapped cells) were prepared for all sample preparation steps using iProChip and analyzed. Compared to the average of 88 proteins from similar studies 35 , our results of an average of 58 proteins presented comparatively fewer proteins from the blank sample (Supplementary Fig. 12 ).…”

Section: Resultscontrasting

confidence: 65%

“…Importantly, the integrated SciProChip-DIA workflow demonstrated sensitive proteome coverage of 1500 ± 131 protein groups from a single PC-9 cell. Compared to recent studies for single-cell profiling, including the identification of 427 proteins using "DISCO" 35 , 1475 protein groups using nanoPOTS with MBR 13 , and ~1000 proteins using isobaric tandem-mass-tag (TMT)-based SCoPE2 12 and SCeptre 24 , this study reported among one of the most sensitive proteome coverages for characterizing a single mammalian cell. Additionally, good analytical merits, including quantitation linearity, wide dynamic range in protein abundances, good between-replicate reproducibility, and low between-run missing values, were systematically benchmarked.…”

Section: Discussionmentioning

confidence: 88%

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Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

et al. 2022

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Single-cell proteomics can reveal cellular phenotypic heterogeneity and cell-specific functional networks underlying biological processes. Here, we present a streamlined workflow combining microfluidic chips for all-in-one proteomic sample preparation and data-independent acquisition (DIA) mass spectrometry (MS) for proteomic analysis down to the single-cell level. The proteomics chips enable multiplexed and automated cell isolation/counting/imaging and sample processing in a single device. Combining chip-based sample handling with DIA-MS using project-specific mass spectral libraries, we profile on average ~1,500 protein groups across 20 single mammalian cells. Applying the chip-DIA workflow to profile the proteomes of adherent and non-adherent malignant cells, we cover a dynamic range of 5 orders of magnitude with good reproducibility and <16% missing values between runs. Taken together, the chip-DIA workflow offers all-in-one cell characterization, analytical sensitivity and robustness, and the option to add additional functionalities in the future, thus providing a basis for advanced single-cell proteomics applications.

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Section: Resultscontrasting

confidence: 65%

Section: Discussionmentioning

confidence: 88%

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

et al. 2022

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“…As various methods have been developed to fabricate DMF chips based on substrates such as silicon wafer, ITO glass, PCB board, and flexible polymers, the DMF technique is able to combine with a variety of analytical methods such as electrochemiluminescence [12], electrochemistry [13], and colorimetric sensing [14]. Currently, the EWOD-based DMF has been widely used in biosensing, environmental monitoring, and food safety, such as single-cell sequencing [2,15], cell invasion monitoring [5], detection of growth factors in embryo culture medium [9], bacterial classification [16], marine pollution monitoring [17], and detection of food nitrite [14].…”

Section: Introductionmentioning

confidence: 99%

Colorimetric Sensing with Gold Nanoparticles on Electrowetting-Based Digital Microfluidics

Luo

Ding

et al. 2021

Micromachines

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Digital microfluidic (DMF) has been a unique tool for manipulating micro-droplets with high flexibility and accuracy. To extend the application of DMF for automatic and in-site detection, it is promising to introduce colorimetric sensing based on gold nanoparticles (AuNPs), which have advantages including high sensitivity, label-free, biocompatibility, and easy surface modification. However, there is still a lack of studies for investigating the movement and stability of AuNPs for in-site detection on the electrowetting-based digital microfluidics. Herein, to demonstrate the ability of DMF for colorimetric sensing with AuNPs, we investigated the electrowetting property of the AuNPs droplets on the hydrophobic interface of the DMF chip and examined the stability of the AuNPs on DMF as well as the influence of evaporation to the colorimetric sensing. As a result, we found that the electrowetting of AuNPs fits to a modified Young–Lippmann equation, which suggests that a higher voltage is required to actuate AuNPs droplets compared with actuating water droplets. Moreover, the stability of AuNPs was maintained during the processing of electrowetting. We also proved that the evaporation of droplets has a limited influence on the detections that last several minutes. Finally, a model experiment for the detection of Hg2+ was carried out with similar results to the detections in bulk solution. The proposed method can be further extended to a wide range of AuNPs-based detection for label-free, automatic, and low-cost detection of small molecules, biomarkers, and metal ions.

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“…It is beyond the scope of this article to explore these three forms of learning approaches in detail. Instead, we focus on supervised learning as this is the most commonly used method in biopeptide prediction [ 217 , 219 ]. Supervised learning methods are used to build and train prediction models for data category values or continuous variables.…”

Section: The Future Of Microfluidicsmentioning

confidence: 99%

Microfluidics for Peptidomics, Proteomics, and Cell Analysis

et al. 2021

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Microfluidics is the advanced microtechnology of fluid manipulation in channels with at least one dimension in the range of 1–100 microns. Microfluidic technology offers a growing number of tools for manipulating small volumes of fluid to control chemical, biological, and physical processes relevant to separation, analysis, and detection. Currently, microfluidic devices play an important role in many biological, chemical, physical, biotechnological and engineering applications. There are numerous ways to fabricate the necessary microchannels and integrate them into microfluidic platforms. In peptidomics and proteomics, microfluidics is often used in combination with mass spectrometric (MS) analysis. This review provides an overview of using microfluidic systems for peptidomics, proteomics and cell analysis. The application of microfluidics in combination with MS detection and other novel techniques to answer clinical questions is also discussed in the context of disease diagnosis and therapy. Recent developments and applications of capillary and microchip (electro)separation methods in proteomic and peptidomic analysis are summarized. The state of the art of microchip platforms for cell sorting and single-cell analysis is also discussed. Advances in detection methods are reported, and new applications in proteomics and peptidomics, quality control of peptide and protein pharmaceuticals, analysis of proteins and peptides in biomatrices and determination of their physicochemical parameters are highlighted.

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Digital microfluidic isolation of single cells for -Omics

Cited by 90 publications

References 71 publications

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

Colorimetric Sensing with Gold Nanoparticles on Electrowetting-Based Digital Microfluidics

Microfluidics for Peptidomics, Proteomics, and Cell Analysis

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