Transcript abundances were examined in single Capitella teleta embryos at three timepoints: 8-cell, 16-cell, and 32-cell stage. Overall design: 12 whole embryos were sequenced individually using CEL-Seq (https://github.com/yanailab/CEL-Seq-pipeline commit version fecc97e ) . There were 4 replicates of 8-cell stage embryos, 3 replicates of 16-cell stage embryos, and 5 replicated of 32-cell stage embryos.