Rainbow-seq: combining cell division lineage tracking with single-cell RNA sequencing for understanding cell fate decision in preimplantation development

Our main question is whether there are reproducible cell-to-cell transcriptome differences in 4-cell embryos that are attributable to their different progenitor cells at the 2-cell stage. If the answer is negative, we wish to test whether there are reproducible cell-to-cell transcriptome differences in 8-cell embryos that are attributable to their different progenitor cells at the 2-cell stage. To address these questions, we developed the Rainbow-seq method that uses fluorescent protein genes to trace cell divisions in preimplantation embryonic development (PED) embryos Mouse strains STOCK Gt(ROSA)26Sortm1(CAG-Brainbow2.1)Cle/J (stock number 013731) and STOCK Tg(CAG-cre/Esr1*)5Amc/J (stock number 004453) were crossed for the production of embryos containing one copy of the Rainbow construct 2.1 and one copy of the gene coding for the CRE protein. Two-cell embryos were collected 46hpi and treated in vitro with 4-Hydroxytamoxifen for two hours, followed by in vitro culture in KSOM media (37°C, 5%CO2, 100% humidity). Embryos were cultured until reaching 4-cell, 8-cell or early blastocyst . stage. The cells of 4- and 8-cell embryos were dissociated for single cell sequencing.