Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Nat Plants. 2023 Jul;9(7):1026-1033. doi: 10.1038/s41477-023-01439-4. Epub 2023 Jun 12.
Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (plant hybridization-based targeted observation of gene expression map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyse 28 cell-type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-sequencing datasets in complex plant tissue.
在原生的三维组织环境中获取单个细胞的复杂反应对于全面理解组织功能至关重要。在这里，我们介绍了 PHYTOMap（基于植物杂交的靶向观察基因表达图谱），这是一种多重荧光原位杂交方法，可在无转基因且低成本的情况下，对整个植物组织中的单细胞和空间进行基因表达的分析。我们将 PHYTOMap 应用于拟南芥根中 28 个细胞类型标记基因的同时分析，并成功鉴定了主要细胞类型，表明我们的方法可以大大加速在复杂植物组织中单细胞 RNA-seq 数据集定义的标记基因的空间图谱绘制。
