ERP104649 PRJEB22925 E-MTAB-6117 Single-cell RNA-seq of the 16-cell stage Ciona embryo Ciona develops according to a stereotyped or invariant lineage. This allowed us to collect precisely defined replicates of all eight blastomeres of the right half of the embryo at the 16-cell stage of Ciona. We manually dissected each embryo, collecting and identifying each cell before library preparation and single-cell RNA-seq to give us a data set of 8 blastomeres x 4 embryos (32 cells). We sequenced these on MiSeq and HiSeq 2500. A fifth embryo was only sequenced on MiSeq and excluded from subsequent analysis. Ciona develops according to a stereotyped or invariant lineage. This allowed us to collect precisely defined replicates of all eight blastomeres of the right half of the embryo at the 16-cell stage of Ciona. We manually dissected each embryo, collecting and identifying each cell before library preparation and single-cell RNA-seq to give us a data set of 8 blastomeres x 4 embryos (32 cells). We sequenced these on MiSeq and HiSeq 2500. A fifth embryo was only sequenced on MiSeq and excluded from subsequent analysis. E-MTAB-6117 in ArrayExpress http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6117 ENA-FIRST-PUBLIC 2020-03-06 ENA-LAST-UPDATE 2017-10-06