Science 365, eaax1971 (2019).

Caenorhabditis elegans has an invariant lineage during development, and is an ideal model organism for studying gene-expression dynamics in different lineages and cell types. Single-cell RNA-seq has been used to profile transcriptomic heterogeneity and changes in C. elegans development, however, challenges such as confounding factors and limited data still exist. To portray a near-complete atlas of C. elegans embryonic transcriptome, Packer et al. generated single-cell RNA-seq data for 86,024 embryonic cells covering 87% of lineage branches. Integration with other data, such as bulk RNA-seq time series and fluorescent reporter imaging data from the EPiC and WormBase, allowed them to manually annotate 93% of cells in the dataset with a cell type or a cell lineage. Detailed analysis of this comprehensive resource revealed transcription factors underlying cell fate determination, global patterns of gene expression, and correlations between cell lineage and the transcriptome.