Fig 1: Immunohistochemical (IHC) and transcriptional analysis of rod and cone photoreceptors for embryonic and adult retina sections of WT and cilia-related mutants. (A) IHC staining of retinal cryosections of WT, and ift88, ift172, b9d2, mks1, tmem67, rpgrip1l, tctn1, tmem216, cc2d2a, cep290, nphp1 and nphp4 mutant embryos at 5 dpf. Dorsal views are shown. Images of IHC staining of cone photoreceptors with Zpr1 (green; inner segment), PNA (red; outer segment) and DAPI (blue; nuclei) in column 1. Higher-magnification images are in column 2. Images of IHC staining of rod photoreceptors with Zpr3 (red; rhodopsin – outer segment if trafficked properly) and nuclei with DAPI (blue) are in column 3. Higher-magnification images are in column 4. Scale bars: 50 µm (columns 1 and 3); 25 µm (columns 2 and 4). (B) The table depicting retinal defects observed in mutant embryos. ift172−/− and ift88−/− results are highlighted by a red box. (C) K-means clustering of log2 normalized counts of the 65 retinal genes. The experiment workflow for how we defined these 65 genes is shown in Fig. S9A. Colored sidebars represent different clustering groups (yellow, blue, red and orange). (D) Representative cryosectioned 3-month-old adult retinae of WT, and viable b9d2, cep290, tmem67, rpgrip1l, tctn1, nphp1 and nphp4 mutants stained with Zpr1/PNA (green/red; column 1), Zpr3 (red; column 2), Pcna (proliferating cells; red; column 3) and L-plastin/4C4 (green; pan-leukocyte marker/red; microglia marker; column 4). Scale bars: 100 µM.