A single-cell 3D spatiotemporal multi-omics atlas from Drosophila embryogenesis to metamorphosis [Part 1]

Please cite the data from the following article: https://doi.org/10.1016/j.cell.2025.05.047.
The development of a multicellular organism is a highly intricate process tightly regulated by numerous genes and pathways in both spatial and temporal manners. Here, we present Flysta3D, a comprehensive multi-omics atlas of the model organism Drosophila, spanning its developmental lifespan from embryo to pupa. Our datasets encompass 3D single-cell spatial transcriptomic, single-cell transcriptomic, and single-cell chromatin accessibility information. By integrating these multi-omics data, we constructed cell state trajectories that uncover the meticulous profiles of tissue development. With a focus on the central nervous system (CNS) and midgut, we dissected the spatiotemporal dynamics of gene regulatory networks, cell type diversity, and morphological changes from a multi-omics perspective. This extensive atlas provides an unprecedentedly rich resource and serves as a systematic platform for studying Drosophila development with integrated multi-omics data at an ultra-high spatiotemporal resolution.
This is part 1 of 3 of the processed matrices generated in this study, containing scStereo-seq matrices for all samples and scRNA-seq matrix.