Integrated single-cell transcriptomic reference atlas of human embryonic development

This record contains processed data and benchmarking resources associated with the study Systematic transcriptomic evaluation of blastoid models of early human development.

The archive includes the integrated single-cell RNA-sequencing reference of human embryo development spanning approximately embryonic day 4 (E4) to E19. The deposited Seurat object contains processed expression data, a UMAP embedding and harmonized cell-level metadata used for Figure 1G, including final cell lineage/cell-type annotations, synchronized developmental-stage annotations and source-dataset identities.

The archive also contains processed high-confidence and unfiltered blastoid Seurat objects, raw and scaled values for the benchmarking metrics presented in Figure 2K, and the source code for the associated Shiny application with the derived data objects required to run it.

The human embryo reference integrates public data from Molè et al. (E-MTAB-8060), Petropoulos et al. (E-MTAB-3929), Zhou et al. (GSE109555), Xiang et al. (GSE136447), and Tyser et al. (E-MTAB-9388). Original sequencing data remain available through their respective repositories and are not redistributed here.

See README.md inside the archive for the complete folder structure, file descriptions, metadata fields and data-loading instructions.

Associated resources:

• Shiny source code
• Interactive Shiny application