Profiling of messenger RNA was done as previously described (Ma et al., 2011). We isolated total RNA from eyecups and retinas. For the control group, we isolated RNA from four biological replicates consisting of a total of ten eyes pooled into four groups (i.e. 2 eyes, 2 eyes, 3 eyes, and 3 eyes). For the A2E-treated group, a total of six eyes were used, pooled into four biological replicates (i.e. 1 eye, 1 eye, 2 eyes and 2 eyes) before isolation of total RNA.

The 167 genes screened mediating inflammation and autophagy were: Chemokine genes: RGD1561905_predicted (C5), Ccl11, Ccl12, Ccl17, Ccl19, Ccl2, Ccl20, Ccl21, Ccl22, Ccl24, Ccl25, Ccl3, Ccl4, Ccl5, Ccl6, Ccl7, Ccl9, Cx3cl1, Cxcl1, Cxcl10, Cxcl11, Cxcl12 (Sdf1), Cxcl2, Cxcl5, Cxcl9, Il13, Pf4. Chemokine receptors: Ccr1, Ccr2, Ccr3, Ccr4, Ccr5, Ccr6, Ccr7, Ccr8, Ccr9, Cx3cr1, Cxcr3, Ccr10, Il8ra, Cxcr2, Xcr1. Cytokine genes: Ifng (IFNγ), Il10, Il11, Il13, Il15, Il16, Il17b, Il18, Il1a, Il1b, Il1f5, Il1f6, Il3, Il4, Il5, Itgam, Itgb2, Lta, Ltb, Mif, Aimp1, Spp1, Tgfb1, Tnf, Cd40lg (Tnfsf5). Cytokine receptors: Ifng (IFNγ), Il10ra, Il13, Il13ra1, Il1r1, Il1r2, Il2rb, Il2rg, Il5ra, Il6r, Il6st, Tnfrsf1a (TNFR1), Tnfrsf1b (TNFR2). Other genes involved in the inflammatory response: Abcf1, Bcl6, Cxcr5, C3, Casp1, Crp, Il1r1, Cxcr2, Tollip. Genes involved in autophagic vacuole formation: Ambra1, Atg12, Atg16l1, Atg4b, Atg4c, Atg5, Atg9a, Becn1, Ctsd, Gabarap, Gabarapl2, Irgm, Map1lc3a, Map1lc3b, Psen1, Rb1cc1, RGD1359310, Rgs19, Tm9sf1, Ulk1, Wipi1. Genes responsible for protein targeting to membrane/vacuole: Atg4b, Atg4c, Gabarap. Genes responsible for protein transport: Atg16l1, Atg16l2, Atg3, Atg4b, Atg4c, Atg7, Atg9a, Gabarap, Gabarapl2, Rab24. Genes involved in protein ubiquitination: Atg3, Atg7, Park2, Park7, Pink1. Genes with protease activity: Atg4b, Atg4c. Co-regulators of autophagy and apoptosis: Akt1, App, Atg12, Atg5, Bad, Bak1, Bax, Bcl2, Bcl2l1 (Bcl-x), Becn1, Bid, Bnip3, Casp3, Casp8 (Flice), Npc1, Cdkn1b (p27Kip1), Cdkn2a (p16Ink4), Cln3, Ctsb, Cxcr4, Dapk1, Eif2ak3, Fadd, Fas (Tnfrsf6), Hdac1, Htt, Ifng, Igf1, Ins2, Mapk8 (Jnk1), Mtor, Nfkb1, Park2, Pik3cg, Prkaa1, Pten, Snca, Sqstm1, Tgfb1, Tgm2, Tnf, Tnfsf10 (Trail), Tp53. Co-regulators of autophagy and the cell cycle: Bax, Cdkn1b (p27Kip1), Cdkn2a (p16Ink4), Mapt, Pim2, Pten, Rb1, Tgfb1, Tp53. Autophagy induction by intracellular pathogens: Eif2ak3, Ifng, Lamp1. Autophagy in response to other intracellular signals: Arsa, Ctss, Dram2 (Tmem77), Eif4g1, Esr1 (ERa), Gaa, Hdac6, Hgs, Mapk14 (p38 Mapk), Pik3c3 (Vps34), Pik3r4, Rps6kb1. Chaperone-mediated autophagy: Hsp90aa1.