Arya Ankish, Tripathi Prabhat, Dubey Nidhi, Aier Imlimaong, Kumar Varadwaj Pritish
Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Jhalwa, Prayagraj, 211015, Uttar Pradesh, India.
Genomics Inform. 2025 May 17;23(1):13. doi: 10.1186/s44342-025-00044-5.
Single-cell RNA-sequencing (scRNA-seq) technology brought about a revolutionary change in the transcriptomic world, paving the way for comprehensive analysis of cellular heterogeneity in complex biological systems. It enabled researchers to see how different cells behaved at single-cell levels, providing new insights into the process. However, despite all these advancements, scRNA-seq also experiences challenges related to the complexity of data analysis, interpretation, and multi-omics data integration. In this review, these complications were discussed in detail, directly pointing at the optimization of scRNA-seq approaches and understanding the world of single-cell and its dynamics. Different protocols and currently functional single-cell databases were also covered. This review highlights different tools for the analysis of scRNA-seq and their methodologies, emphasizing innovative techniques that enhance resolution and accuracy at a single-cell level. Various applications were explored across domains including drug discovery, tumor microenvironment (TME), biomarker discovery, and microbial profiling, and case studies were discussed to explain the importance of scRNA-seq by uncovering novel and rare cell types and their identification. This review underlines a crucial aspect of scRNA-seq in the advancement of personalized medicine and highlights its potential to understand the complexity of biological systems.
单细胞RNA测序（scRNA-seq）技术给转录组学领域带来了革命性的变化，为复杂生物系统中细胞异质性的全面分析铺平了道路。它使研究人员能够在单细胞水平上观察不同细胞的行为，为这一过程提供了新的见解。然而，尽管有这些进展，scRNA-seq在数据分析、解释和多组学数据整合的复杂性方面也面临挑战。在这篇综述中，详细讨论了这些复杂问题，直接指向scRNA-seq方法的优化以及对单细胞世界及其动态的理解。还涵盖了不同的方案和当前可用的单细胞数据库。这篇综述重点介绍了用于scRNA-seq分析的不同工具及其方法，强调了在单细胞水平上提高分辨率和准确性的创新技术。探讨了scRNA-seq在药物发现、肿瘤微环境（TME）、生物标志物发现和微生物分析等领域的各种应用，并通过揭示新的和罕见的细胞类型及其鉴定来讨论案例研究，以解释scRNA-seq的重要性。这篇综述强调了scRNA-seq在个性化医学发展中的一个关键方面，并突出了其理解生物系统复杂性的潜力。
