4D-atlas 发布多物种四维时空转录组数据库
4D-atlas: a multi-species four-dimensional spatiotemporal transcriptomics database spanning development, regeneration, and disease
4D-atlas 是一个面向多物种四维时空转录组的公开数据库，作者称其为首个专门收录此类图谱的公开资源。该库收集并标准化了来自六个物种、15 个代表性数据集的 1629 张空间切片，覆盖 88 个不同时间点，每个数据集含 2–41 个时间点，共超过 2220 万个细胞或空间位点，涵盖胚胎发育、组织再生和疾病进展。除数据收集外，4D-atlas 提供七个交互式分析模块，支持在三维空间加时间维度上探索组织形态发生、空间基因模块、通路活性、调控网络、细胞间通讯、发育轨迹和时间表达模式。作者用统一分析流程整合离散生物学阶段的三维空间结构与分子信息，以支持跨时间和空间的系统研究。
来源：Nucleic Acids Research · doi.org
该数据库把跨物种、跨时间点的空间转录组切片统一整理，并配七个分析模块，便于比较不同发育与疾病阶段的时空动态。
Four-dimensional (4D) spatial transcriptomics, which captures molecular landscapes across both three-dimensional (3D) tissue architecture and temporal progression, is essential for deciphering dynamic biological processes such as development, regeneration, and disease progression. Here, we present 4D-atlas (https://bio-bigdata.hrbmu.edu.cn/4D-Atlas or https://4d-atlas.bio-database.com/), the first publicly accessible database dedicated to multi-species 4D spatiotemporal transcriptomic atlases. 4D-atlas collects and standardizes 1629 spatial slices spanning 88 distinct time points with 2–41 per dataset and over 22.2 million cells or spatial spots from 15 representative datasets across six species, encompassing embryonic development, tissue regeneration, and disease progression. Beyond data collection, 4D-atlas provides seven interactive analytical modules that enable 4D (3D space + time) exploration of tissue morphogenesis, spatial gene modules, pathway activities, regulatory networks, cell–cell communication, developmental trajectories, and temporal expression patterns. Using a unified analytical pipeline to integrate 3D spatial architecture and molecular information across discrete biological stages, 4D-atlas enables systematic investigation of tissue morphogenesis and dynamic regulatory programs across time and space.