| [1] | Fiorentino J, Torres-Padilla M E, Scialdone A. Annu. Rev. Genet., 2020, 54: 167. |
| [2] | Lee H O, Park W Y. Single Cell Genomics for Tumor Heterogeneity. Eds.: Noh D Y, Han W, Toi M. Singapore: Springer, 2021. |
| [3] | Minnema-Luiting J, Vroman H, Aerts J, Cornelissen R. Int. J. Mol. Sci., 2018, 19(4): 1041. |
| [4] | Li X M, Wang C Y. Int. J. Oral Sci., 2021, 13: 36. |
| [5] | Tang F C, Barbacioru C, Wang Y Z, Nordman E, Lee C, Xu N L, Wang X H, Bodeau J, Tuch B B, Siddiqui A, Lao K Q, Surani M A. Nat. Meth., 2009, 6(5): 377. |
| [6] | Gupta R K, Kuznicki J. Cells, 2020, 9(8): 1751. |
| [7] | Simmons S K, Lithwick-Yanai G, Adiconis X, Oberstrass F, Iremadze N, Geiger-Schuller K, Thakore P I, Frangieh C J, Barad O, Almogy G, Rozenblatt-Rosen O, Regev A, Lipson D, Levin J Z. Nat. Biotechnol., 2023, 41(2): 204. |
| [8] | McCracken I R, Taylor R S, De La Cuesta F, Dobie R, Henderson B E, Mountford J C, Caudrillier A, Henderson N C, Ponting C P, Baker A H. Eur. Heart J., 2019, 41(9): 1024. |
| [9] | Zhang Y, Wang D, Peng M, Tang L, Ouyang J, Xiong F, Guo C, Tang Y, Zhou Y, Liao Q, Wu X, Wang H, Yu J, Li Y, Li X, Li G, Zeng Z, Tan Y, Xiong W. J. Exp. Clin. Cancer Res., 2021, 40(1): 81. |
| [10] | Papalexi E, Satija R. Nat. Rev. Immunol., 2018, 18(1): 35. |
| [11] | Drescher H, Weiskirchen S, Weiskirchen R. Biomedicines, 2021, 9(11): 1613. |
| [12] | Emmert-Buck M R, Bonner R F, Smith P D, Chuaqui R F, Zhuang Z P, Goldstein S R, Weiss R A, Liotta L A. Science, 1996, 274(5289): 998. |
| [13] | Wu Y, Zhang K. Nat. Rev. Nephrol., 2020, 16(7): 408. |
| [14] | Cao J, Chen X, Huang S Q, Shi W X, Fan Q, Gong Y L, Peng Y, Wu L L, Yang C Y. Trac Trends Anal. Chem., 2023, 158: 116868. |
| [15] | Pattanayak P, Singh S K, Gulati M, Vishwas S, Kapoor B, Chellappan D K, Anand K, Gupta G, Jha N K, Gupta P K, Prasher P, Dua K, Dureja H, Kumar D, Kumar V. Microfluid. Nanofluid., 2021, 25(12): 99. |
| [16] | Streets A M, Zhang X N, Cao C, Pang Y H, Wu X L, Xiong L, Yang L, Fu Y S, Zhao L, Tang F C, Huang Y Y. Proc. Natl. Acad. Sci. U. S. A., 2014, 111(19): 7048. |
| [17] | Chen Y W, Wang X Q, Na X, Zhang Y K, Cai L F, Song J, Yang C Y. Anal. Chem., 2024, 96(31): 12916. |
| [18] | Pan Y T, Cao W J, Mu Y, Zhu Q Y. Biosensors, 2022, 12(7): 450. |
| [19] | Pensold D, Zimmer-Bensch G. Methods for Single-Cell Isolation and Preparation. Eds.: Yu B, Zhang J, Zeng Y, Li L, Wang X. Singapore: Springer, 2020. |
| [20] | Gross A, Schoendube J, Zimmermann S, Steeb M, Zengerle R, Koltay P. Int. J. Mol. Sci., 2015, 16(8): 16897. |
| [21] | Feng Y Q, Li M. Nanoscale, 2023, 15(32): 13346. |
| [22] | Brunner A D, Thielert M, Vasilopoulou C, Ammar C, Coscia F, Mund A, Hoerning O B, Bache N, Apalategui A, Lubeck M, Richter S, Fischer D S, Raether O, Park M A, Meier F, Theis F J, Mann M. Mol. Syst. Biol., 2022, 18(3): e10798. |
| [23] | Gan C Y, Zhang J Y, Chen B, Wang A, Xiong H Y, Zhao J W, Wang C T, Liang S Z, Feng L. Small, 2024, 20(23): 2307329. |
| [24] | Li Y, Huang Z, Xu L B, Fan Y L, Ping J, Li G C, Chen Y J, Yu C W, Wang Q F, Song T R, Lin T, Liu M M, Xu Y Q, Ai N, Meng X N, Qiao Q, Ji H B, Qin Z, Jin S, Jiang N, Wang M X, Shu S K, Zhang F, Zhang W Q, Liu G H, Chen L M, Jiang L. Nat. Meth., 2025, 22(6): 1199. |
| [25] | Roszkowski M, Mansuy I M. Front. Cell Dev. Biol., 2021, 9 : 648274. |
| [26] | Subramanian Parimalam S, Oguchi Y, Abdelmoez M N, Tsuchida A, Ozaki Y, Yokokawa R, Kotera H, Shintaku H. Anal. Chem., 2018, 90(21): 12512. |
| [27] | Schactler S A, Scheuerman S J, Lius A, Altemeier W A, An D, Matula T J, Mikula M, Kulecka M, Denisenko O, Mar D, Bomsztyk K. BMC Genom., 2023, 24: 446. |
| [28] | Lizardi P M, Engelberg A. Anal. Biochem., 1979, 98(1): 116. |
| [29] | Zhang M X, Zou Y, Xu X, Zhang X B, Gao M X, Song J, Huang P F, Chen Q, Zhu Z, Lin W, Zare R N, Yang C Y. Nat. Commun., 2020, 11: 2118. |
| [30] | Kutluk H, Viefhues M, Constantinou I. Small Sci., 2024, 4(4): 2300206. |
| [31] | He P, Williams B A, Trout D, Marinov G K, Amrhein H, Berghella L, Goh S T, Plajzer-Frick I, Afzal V, Pennacchio L A, Dickel D E, Visel A, Ren B, Hardison R C, Zhang Y, Wold B J. Nature, 2020, 583(7818): 760. |
| [32] | Macosko E Z, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas A R, Kamitaki N, Martersteck E M, Trombetta J J, Weitz D A, Sanes J R, Shalek A K, Regev A, McCarroll S A. Cell, 2015, 161(5): 1202. |
| [33] | Sun J F, Philpott M, Loi D, Li S, Monteagudo-Mesas P, Hoffman G, Robson J, Mehta N, Gamble V, Brown T Jr, Brown T Sr, Canzar S, Oppermann U, Cribbs A P. Nat. Meth., 2024, 21(3): 401. |
| [34] | Becskei A, Rahaman S. Comput. Struct. Biotechnol. J., 2022, 20: 4325. |
| [35] | Abdulmalik O, Lombardi A A, Russell J E. PLOS One, 2012, 7(7): e40827. |
| [36] | Micheel J, Safrastyan A, Aron F, Wollny D. Nat. Commun., 2024, 15: 5858. |
| [37] | Ellefson J W, Gollihar J, Shroff R, Shivram H, Iyer V R, Ellington A D. Science, 2016, 352(6293): 1590. |
| [38] | Li S Q, Sun J, Alles?e R, Datta K, Bao Y, Oliveira G, Forman J, Jin R, Olsen L R, Keskin D B, Shukla S A, Wu C J, Livak K J. Nat. Protoc., 2019, 14(8): 2571. |
| [39] | Hashimshony T, Wagner F, Sher N, Yanai I. Cell Rep., 2012, 2(3): 666. |
| [40] | Aird D, Ross M G, Chen W-S, Danielsson M, Fennell T, Russ C, Jaffe D B, Nusbaum C, Gnirke A. Genome Biol., 2011, 12(2): R18. |
| [41] | Korbie D J, Mattick J S. Nat. Protoc., 2008, 3(9): 1452. |
| [42] | Zhou Y, Jia E T, Sheng Y Q, Qiao Y, Wang Y, Shi H J, Liu Z Y, Pan M, Tu J, Bai Y F, Zhao X W, Ge Q Y, Lu Z H. ACS Appl. Mater. Interfaces, 2022, 14(17): 19154. |
| [43] | Morris J, Singh J M, Eberwine J H. J. Vis. Exp., 2011, 50: e2634. |
| [44] | Sasagawa Y, Hayashi T, Nikaido I. Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods. Eds.: Suzuki Y. Singapore: Springer, 2019. |
| [45] | Popova P G, Lagace M A, Tang G, Blakney A K. Eur. J. Pharm. Biopharm., 2024, 198: 114247. |
| [46] | Uhlen M, Quake S R. Trends Biotechnol., 2023, 41(12): 1565. |
| [47] | Pease J, Sooknanan R. Nat. Meth., 2012, 9(3): i. |
| [48] | Marie R, P?denphant M, Koprowska K, B?rlocher L, Vulders R C M, Wilding J, Ashley N, McGowan S J, van Strijp D, van Hemert F, Olesen T, Agersnap N, Bilenberg B, Sabatel C, Schira J, Kristensen A, Bodmer W, van der Zaag P J, Mir K U. Lab Chip, 2018, 18(13): 1891. |
| [49] | Chaitankar V, Karakülah G, Ratnapriya R, Giuste F O, Brooks M J, Swaroop A. Prog. Retin. Eye Res., 2016, 55: 1. |
| [50] | Tan G, Opitz L, Schlapbach R, Rehrauer H. Sci. Rep., 2019, 9(1): 2856. |
| [51] | Rhoads A, Au K F. Genom. Proteom. Bioinform., 2015, 13(5): 278. |
| [52] | Jain M, Olsen H E, Paten B, Akeson M. Genome Biol., 2016, 17(1): 239. |
| [53] | Goetz J J, Trimarchi J M. Nat. Biotechnol., 2012, 30(8): 763. |
| [54] | Mehling M, Tay S. Curr. Opin. Biotechnol., 2014, 25: 95. |
| [55] | Durruthy-Durruthy R, Ray M. Using Fluidigm C1 to Generate Single-Cell Full-Length cDNA Libraries for mRNA Sequencing. Eds.: DiStefano J K. New York:Springer, 2018. |
| [56] | Kaminski T S, Garstecki P. Chem. Soc. Rev., 2017, 46(20): 6210. |
| [57] | Klein A M, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz D A, Kirschner M W. Cell, 2015, 161(5): 1187. |
| [58] | Bageritz J, Raddi G. Single-Cell RNA Sequencing with Drop-Seq. Eds.: Proserpio V. New York: Springer, 2019. |
| [59] | Zheng G X Y, Terry J M, Belgrader P, Ryvkin P, Bent Z W, Wilson R, Ziraldo S B, Wheeler T D, McDermott G P, Zhu J J, Gregory M T, Shuga J, Montesclaros L, Underwood J G, Masquelier D A, Nishimura S Y, Schnall-Levin M, Wyatt P W, Hindson C M, Bharadwaj R, Wong A, Ness K D, Beppu L W, Deeg H J, McFarland C, Loeb K R, Valente W J, Ericson N G, Stevens E A, Radich J P, Mikkelsen T S, Hindson B J, Bielas J H. Nat. Commun., 2017, 8(1): 14049. |
| [60] | Juzenas S, Goda K, Kiseliovas V, Zvirblyte J, Quintinal-Villalonga A, Siurkus J, Nainys J, Mazutis L. Nucleic Acids Res., 2025, 53(2): gkae1312. |
| [61] | Shum E Y, Walczak E M, Chang C, Christina Fan H. Quantitation of mRNA Transcripts and Proteins Using the BD Rhapsody? Single-Cell Analysis System. Eds.: Suzuki Y. Singapore: Springer, 2019. |
| [62] | Ma?no N, Hauling T, Cappi G, Madaboosi N, Dupouy D G, Nilsson M. Sci. Rep., 2019, 9: 3542. |
| [63] | Chen J, Wang X, Ma A, Wang Q E, Liu B, Li L, Xu D, Ma Q. Nat. Commun., 2022, 13(1): 6494. |
| [64] | Bhagwat N, Dulmage K, Pletcher C H Jr, Wang L, DeMuth W, Sen M E, Balli D, Yee S S, Sa S L, Tong F, Yu L P, Moore J S, Stanger B Z, Dixon E P, Carpenter E L. Sci. Rep., 2018, 8: 5035. |
| [65] | Liu Y X, Fan Z H, Qiao L, Liu B H. Trac. Trends Anal. Chem., 2022, 157: 116822. |
| [66] | Zhu J C, Wang Y C, Chen P, Su H Y, Du W, Liu B F. Sens. Actuat. B Chem., 2019, 283: 685. |
| [67] | Denyer T, Timmermans M C P. Trends Plant Sci., 2022, 27(1): 104. |
| [68] | Sarma M, Lee J, Ma S, Li S, Lu C. Lab Chip, 2019, 19(7): 1247. |
| [69] | Vickovic S, St?hl P L, Salmén F, Giatrellis S, Westholm J O, Mollbrink A, Navarro J F, Custodio J, Bienko M, Sutton L A, Rosenquist R, Frisén J, Lundeberg J. Nat. Commun., 2016, 7: 13182. |
| [70] | Shi S, Baracho G V, Song H W, Acob R A, Ayer A, Widmann S J, Tyznik A J. J. Immunol., 2023, 210(Supplement 1): 251.09. |
| [71] | Wen N, Zhao Z, Fan B Y, Chen D Y, Men D, Wang J B, Chen J. Molecules, 2016, 21(7): 881. |
| [72] | Li G L, Ji Y, Wu Y H, Liu Y S, Li H, Wang Y M, Chi M B, Sun H Y, Zhu H Q. Biosens. Bioelectron., 2023, 237: 115451. |
| [73] | Zhuo Y, Wang Y R, Gao R K, Zhan C B, Liu H C, Liu Y Y, Wang F F, Chen X Z, Feng Y J, Yu L D. Microchem. J., 2025, 212: 113330. |
| [74] | Sauzade M, Brouzes E. Lab Chip, 2017, 17(13): 2186. |
| [75] | Zhang B Y, Xu H, Huang Y Q, Shu W L, Feng H T, Cai J, Zhong J F, Chen Y. Analyst, 2019, 144(24): 7185. |
| [76] | Li R, Zhou M X, Yue C Y, Zhang W K, Ma Y, Peng H L, Hu Z Y, Wei Z W. Lab Chip, 2018, 18(5): 723. |
| [77] | Fang W B, Liu X D, Maiga M, Cao W J, Mu Y, Yan Q, Zhu Q Y. Biosensors, 2024, 14(2): 64. |
| [78] | Kim S C, Clark I C, Shahi P, Abate A R. Anal. Chem., 2018, 90(2): 1273. |
| [79] | Li Z G, Liu A Q, Klaseboer E, Zhang J B, Ohl C D. Lab Chip, 2013, 13(6): 1144. |
| [80] | Kim J, Hong J W, Kim D P, Shin J H, Park I. Lab Chip, 2012, 12(16): 2914. |
| [81] | Cheng Y N, Wang Y, Wang Z Y, Huang L, Bi M Z, Xu W X, Wang W H, Ye X Y. Biomicrofluidics, 2017, 11(2): 024112. |
| [82] | Ruan Q Y, Shi C R, Lin X Y, Ruan W D, Xu M H, Yang C Y, Ren Y K. Chem. Eng. J., 2025, 511: 162099. |
| [83] | Liao Z R, Zhang Y, Li Y R, Miao Y F, Gao S M, Lin F K, Deng Y L, Geng L N. Biosens. Bioelectron., 2019, 126: 697. |
| [84] | Wu X, Li B W, Wang Y D, Xue J C, Zhao H T, Huang Z C, Zheng Z B, Liang N X, Wei Z W. Anal. Chem., 2024, 96(42): 17027. |
| [85] | Sun L, Lehnert T, Gijs M A M, Li S J. Lab Chip, 2022, 22(21): 4224. |
| [86] | Maguire S, Lohman G J S, Guan S X. Nucleic Acids Res., 2020, 48(14): e80. |
| [87] | Zhang Q Q, Xu X, Lin L, Yang J, Na X, Chen X, Wu L L, Song J, Yang C Y. Lab Chip, 2022, 22(10): 1971. |
| [88] | DeLaughter D M. Curr. Protoc. Mol. Biol., 2018, 122: e55. |
| [89] | Li W Y, Bazaz S R, Mayoh C, Salomon R. Curr. Protoc., 2024, 4(2): e963. |
| [90] | Pollen A A, Nowakowski T J, Shuga J, Wang X H, Leyrat A A, Lui J H, Li N Z, Szpankowski L, Fowler B, Chen P L, Ramalingam N, Sun G, Thu M, Norris M, Lebofsky R, Toppani D, Kemp D W II, Wong M, Clerkson B, Jones B N, Wu S Q, Knutsson L, Alvarado B, Wang J, Weaver L S, May A P, Jones R C, Unger M A, Kriegstein A R, West J A A. Nat. Biotechnol., 2014, 32(10): 1053. |
| [91] | Gong H B, Do D, Ramakrishnan R. Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits. Eds.: Raghavachari N, Garcia-Reyero N. New York: Springer, 2018. |
| [92] | Wu A R, Neff N F, Kalisky T, Dalerba P, Treutlein B, Rothenberg M E, Mburu F M, Mantalas G L, Sim S, Clarke M F, Quake S R. Nat. Meth., 2014, 11(1): 41. |
| [93] | Xin Y R, Kim J, Ni M, Wei Y, Okamoto H, Lee J, Adler C, Cavino K, Murphy A J, Yancopoulos G D, Lin H C, Gromada J. Proc. Natl. Acad. Sci. U. S. A., 2016, 113(12): 3293. |
| [94] | Siriwach R, Ngo A Q, Higuchi M, ARIMA K, Sakamoto S, Watanabe A, Narumiya S, Thumkeo D. iScience, 2022, 25(4): 104130. |
| [95] | Arya A, Tripathi P, Dubey N, Aier I, Kumar Varadwaj P. Genom. Inform., 2025, 23: 13. |
| [96] | Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, L?nnerberg P, Linnarsson S. Nat. Meth., 2014, 11(2): 163. |
| [97] | Prakash P G, Kumar N, Gurumurthy R K, Chumduri C. Sci. Data, 2024, 11: 1238. |
| [98] | Li Y Q, Wang W J, Wang D Y, Zhang L C, Wang X Z, He J, Cao L, Li K, Xie H Y. Genes, 2022, 13(12): 2276. |
| [99] | Xin S Y, Liu X, Li Z Y, Sun X C, Wang R, Zhang Z H, Feng X W, Jin L, Li W Y, Tang C Z, Mei W L, Cao Q, Wang H J, Zhang J G, Feng L J, Ye L. Exp. Hematol. Oncol., 2023, 12(1): 49. |
| [100] | Wang C, Lu M Y, Chen C M, Chen J J, Cai Y S, Wang H, Tao L L, Yin W H, Chen J K. Int. Immunopharmacol., 2025, 145: 113752. |
| [101] | Ulbrich J, Lopez-Salmeron V, Gerrard I. BD Rhapsody? Single-Cell Analysis System Workflow: From Sample to Multimodal Single-Cell Sequencing Data. Eds.: Calogero R A, Benes V. New York: Springer, 2023. |
| [102] | Timms J A, Winter S, Hargreaves S, McLornan D P, Platzbecker U, Kordasti S. Blood, 2019, 134(Supplement 1): 2980. |
| [103] | Nguyen R, Vaidyanathan S, Hlathu Z, Zhao X Y, Moskwa J, Acob R A, Gordon C, Wang L, Ayer A. Cancer Res., 2025, 85(8_Supplement 1): 4078. |
| [104] | Ji X H, Miranda M, Suresh S, Bader C S, Zoubeidi A, Meyer E H, Maecker H T. J. Immunol., 2023, 210(Supplement 1): 249.03. |
| [105] | Scheiber A, Trebo M, Pittl A, Heidegger I, Hautz T, Oberhuber R, Trajanoski Z, Augustin F, Sopper S, Wolf D, Pircher A, Salcher S. STAR Protoc., 2024, 5(4): 103475. |
| [106] | Sennikov S, Volynets M, Alrhmoun S, Perik-Zavodskii R, Perik-Zavodskaia O, Fisher M, Lopatnikova J, Shevchenko J, Nazarov K, Philippova J, Alsalloum A, Kurilin V, Silkov A. Front. Immunol., 2024, 15 :1470130. |
| [107] | Hautz T, Salcher S, Fodor M, Sturm G, Ebner S, Mair A, Trebo M, Untergasser G, Sopper S, Cardini B, Martowicz A, Hofmann J, Daum S, Kalb M, Resch T, Krendl F, Weissenbacher A, Otarashvili G, Obrist P, Zelger B, ?fner D, Trajanoski Z, Troppmair J, Oberhuber R, Pircher A, Wolf D, Schneeberger S. Nat. Commun., 2023, 14: 2285. |
| [108] | Szulwach K E, Chen P L, Wang X H, Wang J, Weaver L S, Gonzales M L, Sun G, Unger M A, Ramakrishnan R. PLOS One, 2015, 10(8): e0135007. |