Microfluidics Applications for High-throughput Single Cell Sequencing

Overview

Journal J Nanobiotechnology

Publisher Biomed Central

Specialty Biotechnology

Date 2021 Oct 12

PMID 34635104

Citations 27

Authors

Wen-Min Zhou

Yan-Yan Yan

Qiao-Ru Guo

Hong Ji

Hui Wang

Tian-Tian Xu

Bolat Makabel

Christian Pilarsky

Gen He

Xi-Yong Yu

Jian-Ye Zhang

Affiliations

Soon will be listed here.

Abstract

The inherent heterogeneity of individual cells in cell populations plays significant roles in disease development and progression, which is critical for disease diagnosis and treatment. Substantial evidences show that the majority of traditional gene profiling methods mask the difference of individual cells. Single cell sequencing can provide data to characterize the inherent heterogeneity of individual cells, and reveal complex and rare cell populations. Different microfluidic technologies have emerged for single cell researches and become the frontiers and hot topics over the past decade. In this review article, we introduce the processes of single cell sequencing, and review the principles of microfluidics for single cell analysis. Also, we discuss the common high-throughput single cell sequencing technologies along with their advantages and disadvantages. Lastly, microfluidics applications in single cell sequencing technology for the diagnosis of cancers and immune system diseases are briefly illustrated.

Citing Articles

Microfluidics for the biological analysis of atmospheric ice-nucleating particles: Perspectives and challenges.

Tarn M, Shaw K, Foster P, West J, Johnston I, McCluskey D Biomicrofluidics. 2025; 19(1):011502.

PMID: 40041008 PMC: 11878220. DOI: 10.1063/5.0236911.

Single-Cell Multi-Omics Profiling of Immune Cells Isolated from Atherosclerotic Plaques in Male ApoE Knockout Mice Exposed to Arsenic.

Makhani K, Yang X, Dierick F, Subramaniam N, Gagnon N, Ebrahimian T Environ Health Perspect. 2025; 133(1):17007.

PMID: 39847705 PMC: 11756858. DOI: 10.1289/EHP14285.

Ultrasensitive detection of intact SARS-CoV-2 particles in complex biofluids using microfluidic affinity capture.

Rabe D, Choudhury A, Lee D, Luciani E, Ho U, Clark A Sci Adv. 2025; 11(2):eadh1167.

PMID: 39792670 PMC: 11721714. DOI: 10.1126/sciadv.adh1167.

Combined Dielectric-Optical Characterization of Single Cells Using Dielectrophoresis-Imaging Flow Cytometry.

Arzhang B, Lee J, Kovacs E, Butler M, Salimi E, Thomson D Biosensors (Basel). 2024; 14(12).

PMID: 39727842 PMC: 11674913. DOI: 10.3390/bios14120577.

Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3.

Chuang H, Li R, Huang H, Liu S, Wan C, Chaudhuri S BMC Genomics. 2024; 25(1):1127.

PMID: 39574011 PMC: 11583680. DOI: 10.1186/s12864-024-11036-0.

References

Compton J . Nucleic acid sequence-based amplification. Nature. 1991; 350(6313):91-2. DOI: 10.1038/350091a0. View

Reece A, Xia B, Jiang Z, Noren B, McBride R, Oakey J . Microfluidic techniques for high throughput single cell analysis. Curr Opin Biotechnol. 2016; 40:90-96. PMC: 4975615. DOI: 10.1016/j.copbio.2016.02.015. View

Zhu X, Chu J, Wang Y . Advances in Microfluidics Applied to Single Cell Operation. Biotechnol J. 2017; 13(2). DOI: 10.1002/biot.201700416. View

Faley S, Copland M, Wlodkowic D, Kolch W, Seale K, Wikswo J . Microfluidic single cell arrays to interrogate signalling dynamics of individual, patient-derived hematopoietic stem cells. Lab Chip. 2009; 9(18):2659-64. DOI: 10.1039/b902083g. View

Durruthy-Durruthy R, Ray M . Using Fluidigm C1 to Generate Single-Cell Full-Length cDNA Libraries for mRNA Sequencing. Methods Mol Biol. 2018; 1706:199-221. DOI: 10.1007/978-1-4939-7471-9_11. View

Theberge A, Courtois F, Schaerli Y, Fischlechner M, Abell C, Hollfelder F . Microdroplets in microfluidics: an evolving platform for discoveries in chemistry and biology. Angew Chem Int Ed Engl. 2010; 49(34):5846-68. DOI: 10.1002/anie.200906653. View

Picelli S, Faridani O, Bjorklund A, Winberg G, Sagasser S, Sandberg R . Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 2014; 9(1):171-81. DOI: 10.1038/nprot.2014.006. View

Marie R, Podenphant M, Koprowska K, Baerlocher L, Vulders R, Wilding J . Sequencing of human genomes extracted from single cancer cells isolated in a valveless microfluidic device. Lab Chip. 2018; 18(13):1891-1902. DOI: 10.1039/c8lc00169c. View

Hashimshony T, Wagner F, Sher N, Yanai I . CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012; 2(3):666-73. DOI: 10.1016/j.celrep.2012.08.003. View

10.

Biocanin M, Bues J, Dainese R, Amstad E, Deplancke B . Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip. Lab Chip. 2019; 19(9):1610-1620. DOI: 10.1039/c9lc00014c. View

11.

Malter H . Micromanipulation in assisted reproductive technology. Reprod Biomed Online. 2016; 32(4):339-47. DOI: 10.1016/j.rbmo.2016.01.012. View

12.

Macosko E, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M . Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214. PMC: 4481139. DOI: 10.1016/j.cell.2015.05.002. View

13.

Segaliny A, Li G, Kong L, Ren C, Chen X, Wang J . Functional TCR T cell screening using single-cell droplet microfluidics. Lab Chip. 2018; 18(24):3733-3749. PMC: 6279597. DOI: 10.1039/c8lc00818c. View

14.

Chen Y, Sahoo S, Brien R, Jung S, Humphries B, Lee W . Single-cell RNA-sequencing of migratory breast cancer cells: discovering genes associated with cancer metastasis. Analyst. 2019; 144(24):7296-7309. PMC: 8942075. DOI: 10.1039/c9an01358j. View

15.

Gao C, Zhang M, Chen L . The Comparison of Two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chromium. Curr Genomics. 2021; 21(8):602-609. PMC: 7770630. DOI: 10.2174/1389202921999200625220812. View

16.

Wu A, Neff N, Kalisky T, Dalerba P, Treutlein B, Rothenberg M . Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods. 2013; 11(1):41-6. PMC: 4022966. DOI: 10.1038/nmeth.2694. View

17.

Salomon R, Kaczorowski D, Valdes-Mora F, Nordon R, Neild A, Farbehi N . Droplet-based single cell RNAseq tools: a practical guide. Lab Chip. 2019; 19(10):1706-1727. DOI: 10.1039/c8lc01239c. View

18.

Hummer D, Kurth F, Naredi-Rainer N, Dittrich P . Single cells in confined volumes: microchambers and microdroplets. Lab Chip. 2016; 16(3):447-58. DOI: 10.1039/c5lc01314c. View

19.

Armand E, Li J, Xie F, Luo C, Mukamel E . Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron. 2021; 109(1):11-26. PMC: 7808568. DOI: 10.1016/j.neuron.2020.12.010. View

20.

Liu P, Mathies R . Integrated microfluidic systems for high-performance genetic analysis. Trends Biotechnol. 2009; 27(10):572-81. DOI: 10.1016/j.tibtech.2009.07.002. View