Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their workflows. Maximizing the potential of scRNA-seq requires a proper understanding of the spatiotemporal context of cells. However, positional information is inherently lost during scRNA-seq, limiting its potential to characterize complex biological systems. In this review we highlight how current single-cell analysis pipelines cannot completely recover spatial information, which confounds biological interpretation. Various strategies exist to identify the location of RNA, from classical RNA in situ hybridization to spatial transcriptomics. Herein we discuss the possibility of utilizing this spatial information to supervise single-cell analyses. An integrative approach will maximize the potential of each technology, and lead to insights which go beyond the capability of each individual technology.

植物科学家正在快速将单细胞 RNA 测序 (scRNA-seq) 整合到他们的工作流程中。最大限度地发挥 scRNA-seq 的潜力需要正确了解细胞的时空背景。然而，位置信息在 scRNA-seq 过程中本质上会丢失，限制了其表征复杂生物系统的潜力。在这篇综述中，我们强调当前的单细胞分析流程如何无法完全恢复空间信息，这混淆了生物学解释。存在多种策略来识别 RNA 的位置，从经典的 RNA原位杂交到空间转录组学。在这里，我们讨论利用这种空间信息来监督单细胞分析的可能性。综合方法将最大限度地发挥每种技术的潜力，并带来超越每种技术能力的见解。