Data availabilityDetailed information, resources or reagents associated with this study can be obtained from Y. Lan. The raw data generated in this study have been deposited in the Genome Sequence Archive for Human (GSA-Human) under accession HRA008193. The processed data for this study have been deposited in Figshare at https://doi.org/10.6084/m9.figshare.27004099 (ref. 86). Human in vitro embryo-like single-cell reference datasets for projection were obtained from Array Express (E-MTAB-6819) and the Gene Expression Omnibus (GEO) (GSE136447). Published human CS7 embryo single-cell data are available via Array Express under accession E-MTAB-9388. The spatial transcriptomic data of CS7 embryos that we reanalysed in this study can be accessed from GSA-Human under accession HRA006197, and CS8 spatial transcriptomic data are available under accession HRA005567. Single-cell data of the human yolk sac from CS11 to CS17 stages were downloaded from the NCBI GEO database under accession GSE133345. 10x scRNA-seq data of human CS10, CS11 and CS15 embryos are available from GEO under accession GSE268143. scRNA-seq data of monkey gastrulation and early organogenesis can be accessed from GEO under accession GSE193007. The mouse embryonic single-cell dataset spanning stages E6.5 to E8.5 used in this study is available from Array Express under accession number E-MTAB-6967, and the E10.5 mouse gastrulation dataset can be retrieved from Array Express under accession E-MTAB-6987. scRNA-seq data of human adult erythrocytes and megakaryocytes were downloaded from GEO under accession GSE253355. The hg38 human reference genome was downloaded from https://ftp.ensembl.org/pub/release-115/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz. The genome annotation file was downloaded from https://ftp.ensembl.org/pub/release-94/gtf/homo_sapiens/Homo_sapiens.GRCh38.94.gtf.gz.Code availability