Beyond single cells: microfluidics empowering multiomics analysis

Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002;297(5584):1183–6.

Article  PubMed  CAS  Google Scholar 

Chapman AR, Lee DF, Cai W, Ma W, Li X, Sun W, et al. Correlated gene modules uncovered by high-precision single-cell transcriptomics. Proc Natl Acad Sci USA. 2022;119(51): e2206938119.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet. 2019;20(11):631–56.

Article  PubMed  CAS  Google Scholar 

Shen X, Zhao Y, Wang Z, Shi Q. Recent advances in high-throughput single-cell transcriptomics and spatial transcriptomics. Lab Chip. 2022;22(24):4774–91.

Article  PubMed  CAS  Google Scholar 

Wu AR, Wang J, Streets AM, Huang Y. Single-cell transcriptional analysis. Annu Rev Anal Chem. 2017;10(1):439–62.

Article  CAS  Google Scholar 

Mayer S, Milo T, Isaacson A, Halperin C, Miyara S, Stein Y, et al. The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts. Nat Commun. 2023;14(1):5810.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Wilk AJ, Shalek AK, Holmes S, Blish CA. Comparative analysis of cell–cell communication at single-cell resolution. Nat Biotechnol. 2023. https://doi.org/10.1038/s41587-023-01782-z.

Liu Z, Li JP, Chen M, Wu M, Shi Y, Li W, et al. Detecting tumor antigen-specific T cells via interaction-dependent fucosyl-biotinylation. Cell. 2020;183(4):1117-33.e19.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Vandereyken K, Sifrim A, Thienpont B, Voet T. Methods and applications for single-cell and spatial multi-omics. Nat Rev Genet. 2023;24(8):494–515.

Article  PubMed  CAS  Google Scholar 

Zhu C, Preissl S, Ren B. Single-cell multimodal omics: the power of many. Nat Methods. 2020;17(1):11–4.

Article  PubMed  CAS  Google Scholar 

Deng Y, Finck A, Fan R. Single-cell omics analyses enabled by microchip technologies. Annu Rev Biomed Eng. 2019;21(1):365–93.

Article  PubMed  CAS  Google Scholar 

Prakadan SM, Shalek AK, Weitz DA. Scaling by shrinking: empowering single-cell ‘omics’ with microfluidic devices. Nat Rev Genet. 2017;18(6):345–61.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Xu X, Wang J, Wu L, Guo J, Song Y, Tian T, et al. Microfluidic single-cell omics analysis. Small. 2020;16(9):1903905.

Article  CAS  Google Scholar 

Haque A, Engel J, Teichmann SA, Lönnberg T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Medicine. 2017;9(1):75.

Article  PubMed  PubMed Central  Google Scholar 

Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, et al. Best practices for single-cell analysis across modalities. Nat Rev Genet. 2023;24(8):550–72.

Article  PubMed  CAS  Google Scholar 

Granja JM, Klemm S, McGinnis LM, Kathiria AS, Mezger A, Corces MR, et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat Biotechnol. 2019;37(12):1458–65.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161(5):1202–14.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161(5):1187–201.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zhang M, Zou Y, Xu X, Zhang X, Gao M, Song J, et al. Highly parallel and efficient single cell mRNA sequencing with paired picoliter chambers. Nat Commun. 2020;11(1):2118.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Fan HC, Wang J, Potanina A, Quake SR. Whole-genome molecular haplotyping of single cells. Nat Biotechnol. 2011;29(1):51–7.

Article  PubMed  CAS  Google Scholar 

Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol. 2014;32(10):1053–8.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Cheng Y-H, Chen Y-C, Lin E, Brien R, Jung S, Chen Y-T, et al. Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells. Nat Commun. 2019;10(1):2163.

Article  PubMed  PubMed Central  Google Scholar 

Fan HC, Fu GK, Fodor SPA. Combinatorial labeling of single cells for gene expression cytometry. Science. 2015;347(6222):1258367.

Article  PubMed  Google Scholar 

Han XP, Wang RY, Zhou YC, Fei LJ, Sun HY, Lai SJ, et al. Mapping the mouse cell atlas by Microwell-Seq. Cell. 2018;172(5):1091–107.

Article  PubMed  CAS  Google Scholar 

Dura B, Choi JY, Zhang K, Damsky W, Thakral D, Bosenberg M, et al. scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3′ mRNA profiling. Nucleic Acids Res. 2018;47(3): e16.

Article  PubMed Central  Google Scholar 

Yin K, Zhao M, Lin L, Chen Y, Huang S, Zhu C, et al. Well-Paired-Seq: a size-exclusion and locally quasi-static hydrodynamic microwell chip for single-cell RNA-Seq. Small Methods. 2022;6(7):2200341.

Article  CAS  Google Scholar 

Lin S, Yin K, Zhang Y, Lin F, Chen X, Zeng X, et al. Well-TEMP-seq as a microwell-based strategy for massively parallel profiling of single-cell temporal RNA dynamics. Nat Commun. 2023;14(1):1272.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ng AHC, Chamberlain MD, Situ H, Lee V, Wheeler AR. Digital microfluidic immunocytochemistry in single cells. Nat Commun. 2015;6(1):7513.

Article  PubMed  PubMed Central  CAS  Google Scholar 

de Campos RPS, Rackus DG, Shih R, Zhao C, Liu X, Wheeler AR. “Plug-n-Play” sensing with digital microfluidics. Anal Chem. 2019;91(3):2506–15.

Article  PubMed  Google Scholar 

Ruan Q, Ruan W, Lin X, Wang Y, Zou F, Zhou L, et al. Digital-WGS: Automated, highly efficient whole-genome sequencing of single cells by digital microfluidics. Sci Adv. 2020;6(50):eabd6454.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lamanna J, Scott EY, Edwards HS, Chamberlain MD, Dryden MDM, Peng J, et al. Digital microfluidic isolation of single cells for -omics. Nat Commun. 2020;11(1):5632.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017;8(1):14049.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ruff DW, Dhingra DM, Thompson K, Marin JA, Ooi AT. High-throughput multimodal single-cell targeted DNA and surface protein analysis using the Mission Bio Tapestri platform. In: Ooi AT, editor. Single-cell protein analysis: methods and protocols. Springer, US: New York, NY; 2022. p. 171–88.

Chapter  Google Scholar 

Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet. 2016;17(3):175–88.

Article  PubMed  CAS  Google Scholar 

Huang L, Ma F, Chapman A, Lu S, Xie XS. Single-cell whole-genome amplification and sequencing: methodology and applications. Annu Rev Genom Hum G. 2015;16(1):79–102.

Article  CAS  Google Scholar 

Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA. 2002;99(8):5261–6.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zong C, Lu S, Chapman AR, Xie XS. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science. 2012;338(6114):1622–6.

Article  PubMed  PubMed Central 

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