Slides were incubated overnight in primary antibodies—1:200 rabbit RXRγ (sc-555, lot A1111), 1:150 goat S-sensitive opsin (sc-14363; Santa Cruz Biotechnology, Santa Cruz, CA), 1:500 rabbit S-opsin or M-opsin (AB5407, AB5745; Chemicon International, Temecula, CA), 1:10,000 rabbit TRβ2 (a gift from Lily Ng and Douglas Forrest), or 1:200 rat monoclonal phosphohistone H3 (Ab10543; Novus Biologicals, Littleton, CO)—and for 2 hours in secondary antibodies (1:500 AlexaFluor goat anti-rabbit 568, goat anti-rat 488, donkey anti-rabbit 568, or chicken anti-goat 488; Molecular Probes, Inc., Eugene, OR). To visualize cone outer segments, we incubated sections with FITC-conjugated peanut lectin (Sigma-Aldrich) for 2 hours. Sections were rinsed thoroughly in PBS before they were coverslipped (Fluoromount-G; Southern Biotechnology, Birmingham, AL). Slides were viewed on a confocal microscope (Axioplan 2 or LSM5 Pascal; Carl Zeiss Meditec, Dublin, CA), and photographed with a digital camera (Spot 2.3.1; Diagnostic Instruments, Sterling Heights, MI).
For flatmount studies, retinas were marked on the dorsal side with tissue-marking dye (Cancer Diagnostics, Inc., Birmingham, MI), flattened on a glass slide, fixed with 4% paraformaldehyde for 15 minutes, and fixed for an additional hour in a 24-well plate. Retinas were incubated in primary antibodies at the concentrations noted earlier for 48 hours at 4°C and in secondary antibodies overnight at 4°C. To label all cones, we incubated retinas in FITC-conjugated peanut lectin for 2 hours (PNA; Sigma-Aldrich). Retinas were mounted (Fluoromount-G; Southern Biotechnology) between coverslips separated by an imaging chamber (Secure-Seal; Grace Bio-Laboratories, Bend, OR).