The study presents an updated single-cell reference atlas for the starlet sea anemone *Nematostella vectensis*, a representative of the basally branching Cnidaria. The new resource is based on re-mapping of sequence data to a chromosome-level genome assembly and improved gene annotations. The dataset includes additional samples from the 24 h gastrula, 2d planula, and adult mesentery, expanding the pre-existing dataset. The analyses reveal 127 distinct transcriptomic states, including 47 neuroglandular subtypes and two distinct immune-related profiles. The updated gene annotation significantly improves the mapping of single-cell transcriptome data, making it a valuable resource for the community. The study provides insights into the development and tissue composition of *Nematostella vectensis*, contributing to a better understanding of cnidarian biology and evolutionary comparisons.The study presents an updated single-cell reference atlas for the starlet sea anemone *Nematostella vectensis*, a representative of the basally branching Cnidaria. The new resource is based on re-mapping of sequence data to a chromosome-level genome assembly and improved gene annotations. The dataset includes additional samples from the 24 h gastrula, 2d planula, and adult mesentery, expanding the pre-existing dataset. The analyses reveal 127 distinct transcriptomic states, including 47 neuroglandular subtypes and two distinct immune-related profiles. The updated gene annotation significantly improves the mapping of single-cell transcriptome data, making it a valuable resource for the community. The study provides insights into the development and tissue composition of *Nematostella vectensis*, contributing to a better understanding of cnidarian biology and evolutionary comparisons.