PDF(Pubmed)
Abstract：
This paper introduces a single-cell atlas for pivotal developmental stages in Xenopus, encompassing gastrulation, neurulation, and early tailbud. Notably surpassing its predecessors, the new atlas enhances gene mapping, read counts, and gene/cell type nomenclature. Leveraging the latest Xenopus tropicalis genome version, alongside advanced alignment pipelines and machine learning for cell type assignment, this release maintains consistency with previous cell type annotations while rectifying nomenclature issues. Employing an unbiased approach for cell type assignment proves especially apt for embryonic contexts, given the considerable number of non-terminally differentiated cell types. An alternative cell type attribution here adopts a fuzzy, non-deterministic stance, capturing the transient nature of early embryo progenitor cells by presenting an ensemble of types in superposition. The value of the new resource is emphasized through numerous examples, with a focus on previously unexplored germ cell populations where we uncover novel transcription onset features. Offering interactive exploration via a user-friendly web portal and facilitating complete data downloads, this atlas serves as a comprehensive and accessible reference.
摘要：
本文介绍了一种用于非洲爪鱼关键发育阶段的单细胞图谱，包括胃泌素，神经,和早期尾芽。值得注意的是，超越了它的前辈，新的图集增强了基因定位，读取计数,和基因/细胞类型命名法。利用最新的非洲爪狼基因组版本，除了用于细胞类型分配的高级对齐管道和机器学习之外，此版本与以前的单元格类型注释保持一致，同时纠正命名法问题。采用无偏见的方法进行细胞类型分配被证明特别适合胚胎环境，考虑到相当数量的非终末分化细胞类型。这里的替代细胞类型归属采用模糊，非确定性立场，通过在叠加中呈现类型的集合来捕获早期胚胎祖细胞的瞬时性质。通过许多例子强调了新资源的价值，重点关注以前未开发的生殖细胞群体，在那里我们发现了新的转录开始特征。通过用户友好的门户网站提供交互式探索，并促进完整的数据下载，这个图集是一个全面和方便的参考。
