Single cell RNA seq for Ciona late tailbud embryos

We applied single cell RNA seq with 10x genomics platform to study the cell identity change in Ciona late tailbud embryos. By comparing single cell data from Pax3/7>Foxc amd control embryos, we found ectopic expression of FoxC in BTN cells transformed into PSC cells, which suggest common shared origin of BTNs and PSCs. we injected Pax3/7>Foxc construct into Ciona oocytes, fertilized and let them developed into late tailbud stage along with control. Embryos were dissociated into single cells and loaded into 10x platform for single cell RNA-seq. reads are aligned to Ciona genome with Cell Ranger pipeline.