Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

Gastruloids are three-dimensional aggregates of embryonic stem cells (ESCs) that display key features of mammalian post-implantation development, including germ layer specification and axial organization. Gastruloids have mostly been characterized with microscopy-based approaches, limiting the number of genes that can be explored. It is therefore unclear to what extent gene expression in gastruloids reflects in vivo embryonic expression. Using both single-cell RNA-seq (scRNA-seq) and spatial transcriptomics we systematically compared cell types and spatial expression patterns between mouse gastruloids and mouse embryos. RNA sequencing data from tissue sections isolated from mouse gastruloids (tomo-seq and scRNA-seq) For mGst-Lfng-* samples, each processed data was generated from both run1 and run2 samples, and is linked to the corresponding run1 sample records.

类原肠胚（gastruloids）是胚胎干细胞（embryonic stem cells, ESCs）形成的三维聚集体，可展现哺乳动物植入后发育的关键特征，包括胚层特化与轴向组织构建。既往对类原肠胚的研究多采用基于显微镜的实验手段，这一局限限制了可被探索的基因数量。因此，目前尚不清楚类原肠胚中的基因表达在多大程度上能够反映体内胚胎的基因表达模式。本研究同时采用单细胞RNA测序（single-cell RNA-seq, scRNA-seq）与空间转录组学（spatial transcriptomics）技术，系统比较了小鼠类原肠胚与小鼠胚胎的细胞类型及空间表达模式。本研究的RNA测序数据来源于从小鼠类原肠胚中分离的组织切片，涵盖tomo-seq与scRNA-seq两种技术路径。针对mGst-Lfng-*系列样本，每份经处理的数据均由run1与run2样本共同生成，并与对应run1样本的记录相关联。