Identification of cell surface markers expressed by candidate progenitor populations. (a) A scheme of the approach for systematic identification of hESC-derived progenitors, including: (i) flow cytometry-based screen of candidate progenitor populations in self-renewing and differentiating (BMP4- or retinoic acid–treated) cultures, and (ii) lineage analysis based on expression of ~100 early embryonic genes and genome-wide transcriptional profiling. (b–e) Representative FACS plots for few of the markers (Percentages of subpopulations are shown). (b) Labeling of CM-treated cells with novel and established markers of undifferentiated cells (CD100 and Tra-1–81, respectively) revealed negative subpopulations of putative progenitors. (c) CXCR4+ and SSEA-1+ subpopulations within CM-treated cultures. (d) APA and ROR2 are expressed by emerging progenitor populations in BMP4-treated cultures. (e) CD173 and CD133 expression profiles reveal large population shifts in response to treatments with BMP4 and retinoic acid. Red, green and blue lines correspond to CM, retinoic acid and BMP4 treatments, respectively. Gray dotted lines are isotype controls.