The spatial and temporal atlas of gene expression in human embryo at early gestation is critical in understanding embryo development, organogenesis and disease origins. Here, we obtained the spatial-temporal transcriptome from the 77 sagittal sections of 13 human embryos at 12-23 Carnegie stage (CS) by Stereo-seq, established the development trajectory/regulatory profiling of 50 organs, and identified the top organ-specific regulons with the highest score as the potential organ-identity regulators. The atlas refines the key organs/cell types that are vulnerable to virus infection and genetic disorders. We found dynamic changes of imprinting gene expression in specific organs at different stages. Our work, for the first time, revealed the time-lapse and spatial transcriptome dynamics of human embryogenesis after gastrulation.
Jiexue Pan, Hefeng Huang et al. Spatiotemporal transcriptome atlas of human embryos after gastrulation. bioRxiv 2023.04.22.537909; doi: https://doi.org/10.1101/2023.04.22.537909
MOSTA database has a total of 53 sagittal sections from C57BL/6 mouse embryos at E9.5 (~7.1 mm2), E10.5 (~11.5 mm2), E11.5 (~18.8 mm2), E12.5 (~32.1 mm2), E13.5 (~48.4 mm2), E14.5 (~64.1 mm2), E15.5 (~70.8 mm2) and E16.5 (~76.1 mm2) using Stereo-seq. For E9.5-E15.5 stages, four to six sections were included from different replicates. As for E16.5, 17 sagittal sections were profiled from two biological replicates, with 13 sections from one single embryo, allowing coverage of all major organs/tissues. In the MOSTA, we provide the spatial map showing the gene expression, gene co-expression modules and regulons in each embryo sagittal sections. Our panoramic atlas will allow in-depth investigation of longstanding questions concerning mammalian development.
Chen, A., Liao, S., Cheng, M., Ma, K., Wu, L., Lai, Y., ... & Wang, J. (2022). Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell, 185(10), 1777-1792. DOI: 10.1016/j.cell.2022.04.003
Vertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period. A major challenge in understanding this process is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell fate decisions. Here, we employed Stereo-seq to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryos. We profiled 91 embryo sections covering six critical time points during the first 24 hours of development, obtaining a total of 152,977 spots at a resolution of 10x10x15 µm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell fate transitions and molecular changes during zebrafish embryogenesis. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.
Liu, C., Li, R., Li, Y., Lin, X., Zhao, K., Liu, Q., ... & Liu, L. (2022). Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis. Developmental Cell, 57(10), 1284-1298. DOI: 10.1016/j.devcel.2022.04.009
Here we have analysed stem cell-derived cerebral organoids using single-cell transcriptomics and accessible chromatin profiling to investigate gene-regulatory changes that are specific to humans. Our data provide a temporal cell atlas of great ape forebrain development, and illuminate dynamic gene-regulatory features that are unique to humans.
This database is intended to curate 3D spatial transcriptomes of a human gastrulating embryo at Carnegie stage(CS) 8, equivalent to 18-19 days post-fertilization by Stereo-seq. For currently available data, the human CS8 embryo was collected and subjected to cryosection to generate 10 μm thick slices from the rostral side to the caudal side. All slices were applied to Stereo-seq chips to capture their 2D spatial transcriptomes. All the 2D spatial transcriptomes were combined to recreate their 3D spatial transcriptomes and reconstruction 3D CS8 human embryo model. With these data, one could visualize and analyze spatial expression patterns of genes of interest, 3D reconstruct cluster-specific spatial transcriptomes by clustering and annotation, identify cell signaling pathways and gene regulatory networks, examine gene functions in their intact spatial context, provide a unique opportunity to explore the critical cellular and molecular features of gastrulating events, etc.
Xiao Z, Cui L, Yuan Y, He N, Xie X, Lin S, Yang X, Zhang X, Shi P, Wei Z, Li Y, Wang H, Wang X, Wei Y, Guo J, Yu L. 3D reconstruction of a gastrulating human embryo. Cell. 2024 May 23;187(11):2855-2874.e19. doi: 10.1016/j.cell.2024.03.041.
The HDBR Atlas is a unique resource which aims to facilitate the understanding of the development of the human embryo and fetus.
The atlas began as the Electronic Atlas of the Developing Human Brain (EADHB), which was funded by the US National Institutes of Health (NIH) Human Brain Project (grant numbers: HD39928-02 followed by R01 MH070370).
The long-term aim of this work was to create a digital atlas comprising 3D reconstructions from Carnegie Stage 12 to 23, generated using Optical Projection Tomography (OPT; Sharpe et al 2002), and annotations of the 3D models linked to an anatomical database.
The digital atlas was also linked to a gene expression database that was developed from the Edinburgh Mouse Atlas Project gene expression database (EMAGE). Again, the major funder was NIH, as above, with additional funding from EU FP6 (DGEMap, contract number 011993).
With the agreement of the funders, both the digital atlas and the gene expression database were brought together on the HuDSeN website and became the HuDSeN Electronic Atlas of the Developing Human and HuDSeN Human Gene Expression Spatial Database.
Currently the MRC/Wellcome Trust-funded HDBR project is supporting the atlas and gene expression database, and the name has been changed to the HDBR Atlas to reflect this.
In the future, the HDBR Atlas aims to provide the wider scientific, educational and medical communities with a dynamic tool for documenting and analyzing gene expression patterns and morphological changes during human embryonic and fetal development.