美国华盛顿大学Cole Trapnell等研究人员合作开发出胚胎尺度的单细胞空间转录组学技术。相关论文于2021年7月2日发表在《科学》杂志上。

研究人员报道了sci-Space，它保留了单细胞分辨率，同时解决了更大规模的空间异质性。将sci-Space应用于发育中的小鼠胚胎，研究人员捕获了大约120,000个细胞核的近似空间坐标和整个转录组。研究人员鉴定了数千个表现出解剖学模式表达的基因，并利用空间信息来注释了细胞亚型，从而揭示了细胞类型在空间模式化程度方面存在很大差异，并最终揭示了假时间与分化神经元迁移模式之间的相关性。

研究人员预计sci-Space将促进构建空间分辨的哺乳动物发育单细胞图谱。

据了解，基因表达的空间模式表现在从局部（例如，细胞间相互作用）到全局（例如，体轴模式）的范围内。然而，当前的空间转录组学方法要么平均了局部环境，要么仅限于有限的视野。

附：英文原文

Title: Embryo-scale, single-cell spatial transcriptomics

Author: Sanjay R. Srivatsan, Mary C. Regier, Eliza Barkan, Jennifer M. Franks, Jonathan S. Packer, Parker Grosjean, Madeleine Duran, Sarah Saxton, Jon J Ladd, Malte Spielmann, Carlos Lois, Paul D. Lampe, Jay Shendure, Kelly R. Stevens, Cole Trapnell

Issue&Volume: 2021/07/02

Abstract: Spatial patterns of gene expression manifest at scales ranging from local (e.g., cell-cell interactions) to global (e.g., body axis patterning). However, current spatial transcriptomics methods either average local contexts or are restricted to limited fields of view. Here, we introduce sci-Space, which retains single-cell resolution while resolving spatial heterogeneity at larger scales. Applying sci-Space to developing mouse embryos, we captured approximate spatial coordinates and whole transcriptomes of about 120,000 nuclei. We identify thousands of genes exhibiting anatomically patterned expression, leverage spatial information to annotate cellular subtypes, show that cell types vary substantially in their extent of spatial patterning, and reveal correlations between pseudotime and the migratory patterns of differentiating neurons. Looking forward, we anticipate that sci-Space will facilitate the construction of spatially resolved single-cell atlases of mammalian development.

DOI: 10.1126/science.abb9536

Source: https://science.sciencemag.org/content/373/6550/111