Balasubramanian R, Min X, Quinn PMJ, Giudice QL, Tao C, Polanco K, Makrides N, Peregrin J, Bouaziz M, Mao Y, Wang Q, Costa BL, Buenaventura D, Wang F, Ma L, Tsang SH, Pierre JF, Zhang X. 2021. Phase transition specified by a binary code patterns the vertebrate eye cup. Science Advances. https://www.science.org/doi/10.1126/sciadv.abj9846. We performed single-cell RNA-sequencing (scRNAseq) of E13.5 mouse eye cups. Taking advantage of an IRES-GFP cassette embedded in the Pax6 α-Cre driver, we used flow cytometry to enrich for Cre/GFP-expressing cells from peripheral retinae and sequenced 6,628 control and 4,607 α-Cre;Fgfr1flox/flox;Fgfr2flox/flox mutant cells. In addition to retinal progenitor cells (RPC-1 to 4), neurogenic cells (Ngn-1, 2 and boundary) and differentiated retinal neurons (retinal ganglion cells (RGC), amacrine/horizontal cells (AC/HC) and photoreceptor cells (PRC), we were also able to discern three clusters that formed a separate branch connected to the RPC clusters, diametrically opposite to the branch of retinal neurons. RNA velocity analysis identified the differentiation path from the RPC to either the neural retina (NR) or the ciliary margin (CM) fates, which correlated with the transitioning of the cell cycle from the S phase via the G2M to the G1 phase. Our study demonstrated that FGF signaling is required for the self-renew and differentiate of CM progenitor cells.