Sci-Space E14 Mouse Embryo Data

Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections. Combinatorially indexed single cell TNA sequencing libraries. Each read contains a combination of PCR indices and a 3-prime barcode that uniquely identify the reads from a single cell. Sequenced molecules consist of both barcoded cDNA and barcoded synthetic hash-oligo molecules used to mark the spatial position from which a cell is derived.基因表达的空间模式横跨多个尺度，其形成同时受局部（如细胞间相互作用）与全局（如组织、器官）微环境的调控。然而，当前绝大多数用于基因表达谱分析的原位（in situ）方法，要么会对局部微环境进行平均化处理，要么受限于有限的视场范围。为此，我们研发了sci-Space技术：这是一种尺度灵活的方法，可在保留单细胞分辨率的同时，解析大尺度下基因表达的空间异质性。作为概念验证，我们将sci-Space应用于发育中的小鼠胚胎（E14期），通过全胚胎连续切片获取了经基因表达谱分析的细胞的近似空间坐标。本研究采用组合索引式单细胞TNA测序文库。每一条测序读段均包含PCR索引与3'端条形码的组合序列，可唯一标识来自单个细胞的读段。测序得到的分子同时包含带有条形码的cDNA，以及带有条形码的合成哈希寡核苷酸（hash-oligo）分子——这类分子可用于标记细胞来源的空间位置。