To access the data, click or select the words “Appendix 9.” Expression profiles of key genes were assessed at days 0, 6, 30, 40, and 59 during the photoreceptor (PhR) differentiation protocol in Experiment 2 (orange) and Experiment 3 (green). Data are presented as fold-change values normalized to the reference gene GAPDH and scaled to the maximum expression level for each gene. The graphs illustrate temporal expression patterns, including early expression of the pluripotency marker OCT4, followed by the eye-field marker OTX2, activation of the neural retinal progenitor marker VSX2, and early photoreceptor lineage markers PRDM1, CRX, RCVRN and NR2F2. Quantitative PCR analysis across differentiation timepoints revealed distinct temporal patterns in gene expression associated with the transition from pluripotent hIPSCs to photoreceptor (PhR) progenitors. Expression of the pluripotency marker OCT4 declined sharply by day 9 (D9), confirming early exit from the pluripotent state. The retinal specification marker OTX2 peaked at D9 before gradually decreasing, with experiment-specific variation in the rate of decline. VSX2, a marker of retinal progenitor cells, showed temporally distinct expression profiles between experiments, suggesting differences in progenitor proliferation dynamics. PRDM1, associated with PhR lineage commitment, exhibited variable expression patterns, indicating experiment-dependent timing of PhR progenitor emergence. The photoreceptor transcription factor CRX displayed fluctuating expression peaks and declines, reflecting variability in post-mitotic PhR specification. Photoreceptor markers NR2F2 and RCVRN consistently peaked at D30, followed by a tapering phase. These findings underscore key regulatory windows and inter-experimental variability in PhR differentiation trajectories.