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<p>Droplet-based single-cell RNA sequencing (scRNA-seq) has redefined biological research by resolving cellular heterogeneity with an unprecedented precision. This review synthesizes the technological evolution of the 10× Genomics Chromium platform, its Gel Bead-in-Emulsion (GEM)s technology, and end-to-end workflows, while critically addressing persistent challenges, such as cell capture variability (30–75% efficiency), barcode collisions (&lt; 5% multiplet rates), and mRNA capture limitations (10–50% efficiency). We spotlight two transformative applications: (1) cancer research, where scRNA-seq unveils rare circulating tumor cells (CTCs) and dynamic tumor microenvironments, and (2) reproductive medicine, enabling breakthroughs in primordial germ cell (PGC) epigenetics and pre-implantation diagnostics. Unlike prior reviews, we systematically evaluated innovative solutions-including UMIs, computational demultiplexing, and microfluidic cost-reduction strategies (40–60% savings)-and propose a roadmap for integrating spatial transcriptomics and multi-omics approaches. Looking ahead, we identify three frontiers poised to redefine the field: (i) single-cell epigenome-transcriptome co-profiling, (ii) AI-driven analysis of multimodal datasets, and (iii) scalable microfluidics for clinical adoption. This review is of key significance in bridging cutting-edge technology with translational impact in oncology and reproductive biology, while outlining a roadmap for the evolution of the field.</p> Graphical abstract <p></p>

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Droplet-based single-cell RNA sequencing: decoding cellular heterogeneity for breakthroughs in cancer, reproduction, and beyond

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月14日

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  • Haoxuan Luo,
  • Ansar Hussain,
  • Musavir Abbas,
  • Lun Yuan,
  • Youfeng Shen,
  • Ziyuan Zhang,
  • Guorong Sun,
  • Xiujuan Yin,
  • Shan Huang

摘要

Droplet-based single-cell RNA sequencing (scRNA-seq) has redefined biological research by resolving cellular heterogeneity with an unprecedented precision. This review synthesizes the technological evolution of the 10× Genomics Chromium platform, its Gel Bead-in-Emulsion (GEM)s technology, and end-to-end workflows, while critically addressing persistent challenges, such as cell capture variability (30–75% efficiency), barcode collisions (< 5% multiplet rates), and mRNA capture limitations (10–50% efficiency). We spotlight two transformative applications: (1) cancer research, where scRNA-seq unveils rare circulating tumor cells (CTCs) and dynamic tumor microenvironments, and (2) reproductive medicine, enabling breakthroughs in primordial germ cell (PGC) epigenetics and pre-implantation diagnostics. Unlike prior reviews, we systematically evaluated innovative solutions-including UMIs, computational demultiplexing, and microfluidic cost-reduction strategies (40–60% savings)-and propose a roadmap for integrating spatial transcriptomics and multi-omics approaches. Looking ahead, we identify three frontiers poised to redefine the field: (i) single-cell epigenome-transcriptome co-profiling, (ii) AI-driven analysis of multimodal datasets, and (iii) scalable microfluidics for clinical adoption. This review is of key significance in bridging cutting-edge technology with translational impact in oncology and reproductive biology, while outlining a roadmap for the evolution of the field.

Graphical abstract