These data complement GEO accession GSE60478, a time-course of Mnemiopsis leidyi developmental gene expression for hours 0-13 and hour 20. The data here provide additional replicates for 0-13 and 20 hours as well as new timepoints 14–19. As in the original study (Levin et al. 2016 PMID: 26886793) data are from single embryos using the Cel-Seq (Single-Cell RNA-Seq by Multiplexed Linear Amplification PMID:22939981). Embryo processing, sequencing and sequence processing were performed in the same manner as the original analyses (GEO accession GSE60478) so these data should be completely compatible with that study. Overall design: single embryo samples a time-course of Mnemiopsis leidyi developmental gene expression for 0-13 and 20 hours as well as new timepoints 14-19