Supporting Information

Home , CRX (gene), CSDA (gene), EXT1, NRL (gene)

Jia et al. 10.1073/pnas.0902425106

Fig. S1. Crx expression in RorbϪ/Ϫ mice. (A) In situ hybridization of Crx at P6, P14, and P31 showing weaker and disorganized expression of Crx mRNA in RorbϪ/Ϫ mice at postnatal ages. Blue bars indicate that the ONBL (P6) and ONL (P14, P31) are narrower in RorbϪ/Ϫ mice and lie adjacent to the RPE (arrowhead) because inner and outer segments are missing. Crx expression is detected in a relatively more dispersed pattern in RorbϪ/Ϫ mice than in ϩ/ϩ mice because of abnormalities in retinal cell migration and retinal layering. The weaker expression reﬂects in part the loss of photoreceptor numbers in RorbϪ/Ϫ mice. (Scale bar, 50 ␮m in all panels). (B) Real time PCR showing reduced expression levels of Crx mRNA in RorbϪ/Ϫ mice at postnatal ages indicated.

Jia et al. www.pnas.org/cgi/content/short/0902425106 1of10 Fig. S2. Cell apoptosis in wild-type and RorbϪ/Ϫ retina from E16 to P23. The numbers of anti-caspase 3 positive cells were counted in the ONL and INLϩGCL separately on 3 adjacent 10 ␮m mid-retina sections for 3 ϩ/ϩ and 3 RorbϪ/Ϫ mice. Error bars represent the standard deviation. Abbreviations: ONBL, outer neuroblast layer; INBL, inner neuroblast layer; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer. *, P Ͻ 0.05, **, P Ͻ 0.001 by two-tailed Student’s t test. Data from the ϩ/ϩ are consistent with data previously described by [Young RW (1984) Cell death during differentiation of the retina in the mouse. J Comp Neurol 229:362–373].

Jia et al. www.pnas.org/cgi/content/short/0902425106 2of10 Table S1. Average fold changes of selected photoreceptor genes in retina of Rorb؊/؊, Rorb؊/؊;CrxpNrl, and Nrl؊/؊ mice at P28 determined by microarray and qPCR analyses Expression NrlϪ/Ϫ RorbϪ/Ϫ RorbϪ/Ϫ;CrxpNrl RorbϪ/Ϫ RorbϪ/Ϫ;CrxpNrl Gene Symbol Pattern Gene Title vs. WT vs. WT vs. RorbϪ/Ϫ vs. WT vs. RorbϪ/Ϫ

ROD enriched Rho rod rhodopsin Ϫ165.8 Ϫ8.3 2.1 Ϫ7.0 2.6 Pde6b rod phosphodiesterase 6B, cGMP, rod Ϫ19.2 Ϫ24.4 4.5 Ϫ60.4 10.2 receptor, beta polypeptide Cnga1 rod cyclic nucleotide gated channel Ϫ266.1 Ϫ19.8 3.6 Ϫ9.0 2.6 alpha 1 Nr2e3 rod nuclear receptor subfamily 2, Ϫ101.0 Ϫ18.0 3.9 Ϫ8.4 3.0 group E, member 3 Nrl rod neural retina leucine zipper gene Ϫ480.9 Ϫ13.3 2.5 Ϫ14.8 2.6 Gnat1 rod guanine nucleotide binding Ϫ712.6 Ϫ5.7 2.5 Ϫ9.5 2.6 protein, alpha transducing 1 Slc24a1 rod solute carrier family 24 Ϫ46.4 Ϫ16.5 3.1 Ϫ14.6 3.2 (sodium/potassium/calcium exchanger), member 1 Rdh12 rod Ͼ cone retinol dehydrogenase 12 Ϫ4.5 Ϫ5.4 Ϫ1.2 Ϫ8.8 1.3 Rom1 rod ϭ cone rod outer segment membrane Ϫ3.3 Ϫ3.8 Ϫ1.0 Ϫ3.8 1.2 protein 1 Rp1 h rod ϭ cone retinitis pigmentosa 1 homolog Ϫ2.9 Ϫ3.4 Ϫ1.3 Ϫ5.5 1.8 (human) Gngt1 rod ϭ cone guanine nucleotide binding Ϫ2.2 Ϫ2.8 Ϫ1.8 Ϫ1.6 1.3 protein (G protein), gamma transducing activity polypeptide 1 Rgs9bp rod Ͼ cone regulator of G-protein signalling Ϫ2.2 Ϫ3.1 Ϫ1.5 Ϫ4.1 Ϫ1.2 9 binding protein Pias3 rod enriched protein inhibitor of activated -- - Ϫ2.6 1.5 STAT 3 CONE enriched Opn1 sw cone opsin 1 (cone pigments), 14.6 4.6 Ϫ41.0 2.6 Ϫ41.7 short-wave-sensitive Opn1mw cone opsin 1 (cone pigments), 1.6 2.5 Ϫ26.4 3.8 Ϫ122.0 medium-wave-sensitive Arr3 cone Ͼ rod arrestin 3, retinal 5.1 4.2 Ϫ23.9 6.2 Ϫ16.4 Gnat2 cone guanine nucleotide binding 5.2 4.1 Ϫ10.6 4.1 Ϫ11.6 protein, alpha transducing 2 Gnb3 cone ϩ bipolar guanine nucleotide binding 4.2 2.9 Ϫ2.9 3.2 Ϫ2.9 protein, beta 3 Pde6 h cone phosphodiesterase 6H, 5.7 4.3 Ϫ25.6 5.1 Ϫ2.3 cGMP-speciﬁc, cone, gamma Thrb2 cone thyroid hormone receptor beta 2 - - - 7.6 Ϫ126.0 Rxrg Cone ϩ retinoid X receptor gamma 6.4 4.5 Ϫ2.0 4.0 Ϫ2.3 amacrine Gngt2 cone guanine nucleotide binding 8.7 5.8 Ϫ4.5 6.4 Ϫ4.5 protein (G protein), gamma transducing activity polypeptide 2 Pcdh15 cone Ͼ rod protocadherin 15 3.7 2.3 Ϫ4.5 2.3 Ϫ3.8 Elovl2 cone Ͼ rod elongation of very long chain 4.4 2.9 Ϫ6.3 2.6 Ϫ3.9 fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2

Cone or rod expression assignments are based mainly on categories given in refs. 1, 2, with additional information for Rp1 h and Pias3 given in refs. 3, 4.

1. Corbo JC, Cepko CL (2005) A Hybrid Photoreceptor Expressing Both Rod and Cone Genes in a Mouse Model of Enhanced S-Cone Syndrome. PLoS Genet 1:e11. 2. Corbo JC, Myers CA, Lawrence KA, Jadhav AP, Cepko CL (2007) A typology of photoreceptor gene expression patterns in the mouse. Proc Natl Acad Sci USA 104:12069–74. 3. Onishi A, Peng G, Hsu C, Alexis U, Chen S, Blackshaw S (2009) Pias3-Dependent SUMOylation Directs Rod Photoreceptor Development. Neuron 61:234–246. 4. Liu Q, Zhou J, Daiger SP, Farber DB, Heckenlively JR, Smith JE, Sullivan LS, Zuo J, Milam AH, Pierce EA (2002) Identiﬁcation and subcellular localization of the RP1 protein in human and mouse photoreceptors. Invest Ophthalmol Vis Sci 43:22–32.

Jia et al. www.pnas.org/cgi/content/short/0902425106 3of10 Table S2. Average fold changes of more than two fold differentially expressed genes common in Rorb؊/؊ and Nrl؊/؊ retina determined by microarray RorbϪ/Ϫ;CrxpNrl Gene Symbol Gene Name RorbϪ/Ϫ vs WT NrlϪ/Ϫ vs WT to RorbϪ/Ϫ (ratio)

Opn1 sw opsin 1 (cone pigments), short-wave-sensitive 4.61 14.61 0.01 Clca3 chloride channel calcium activated 3 23.02 21.27 0.03 Arr3 arrestin 3, retinal 4.20 5.10 0.04 Pde6 h phosphodiesterase 6H, cGMP-specific, cone, gamma 3.86 4.70 0.04 Fabp7 fatty acid binding protein 7, brain 14.25 36.24 0.07 Kcne2 potassium voltage-gated channel, Isk-related subfamily, gene 2 2.88 3.35 0.08 Tph1 tryptophan hydroxylase 1 16.92 3.03 0.08 Pde6c phosphodiesterase 6C, cGMP specific, cone, alpha prime 5.94 8.91 0.09 Eya1 eyes absent 1 homolog (Drosophila) 11.59 15.30 0.09 Gnat2 guanine nucleotide binding protein, alpha transducing 2 4.08 5.20 0.09 Socs3 suppressor of cytokine signaling 3 12.20 12.32 0.10 Crxos1 Crx opposite strand transcript 1 3.14 4.33 0.10 A230097K15Rik RIKEN cDNA A230097K15 gene 10.01 7.95 0.11 Otop3 otopetrin 3 12.79 13.44 0.11 Gulo gulonolactone (L-) oxidase 4.11 11.43 0.12 Casp7 caspase 7 3.28 4.32 0.12 Myocd myocardin 12.25 11.41 0.13 Pik3ap1 phosphoinositide-3-kinase adaptor protein 1 15.79 10.26 0.14 Akr1b8 aldo-keto reductase family 1, member B8 6.53 7.64 0.14 Adrb1 adrenergic receptor, beta 1 4.41 5.49 0.14 Tmem20 transmembrane protein 20 7.46 3.48 0.15 Elovl2 elongation of very long chain fatty acids (FEN1/Elo2, 2.87 4.43 0.16 SUR4/Elo3, yeast)-like 2 4921511K06Rik RIKEN cDNA 4921511K06 gene 3.90 6.64 0.16 Abi3 ABI gene family, member 3 6.42 18.55 0.16 Cngb3 cyclic nucleotide gated channel beta 3 9.54 14.59 0.16 Mpp6 membrane protein, palmitoylated 6 (MAGUK p55 subfamily 5.03 3.81 0.17 member 6) Gngt2 guanine nucleotide binding protein (G protein), gamma 5.79 8.72 0.17 transducing activity polypeptide 2 Mapk4 mitogen-activated protein kinase 4 4.62 4.43 0.17 Cckbr cholecystokinin B receptor 8.46 6.54 0.17 Gzmm granzyme M (lymphocyte met-ase 1) 2.70 5.78 0.18 4930554H23Rik RIKEN cDNA 4930554H23 gene 3.70 8.04 0.18 Dnaic1 dynein, axonemal, intermediate chain 1 5.29 3.00 0.19 Gckr glucokinase regulatory protein 7.94 2.71 0.20 Parvb parvin, beta 5.82 7.82 0.21 Lrfn2 leucine rich repeat and fibronectin type III domain containing 2 3.69 3.57 0.21 Crp C-reactive protein, pentraxin-related 4.44 6.19 0.21 Rgl3 ral guanine nucleotide dissociation stimulator-like 3 5.53 8.20 0.21 2310007A19Rik RIKEN cDNA 2310007A19 gene 6.92 8.08 0.21 Klhl4 kelch-like 4 (Drosophila) 8.43 5.97 0.23 Ece1 endothelin converting enzyme 1 4.35 4.65 0.24 Cdk6 cyclin-dependent kinase 6 5.73 5.09 0.24 Fin15 fibroblast growth factor inducible 15 3.60 4.07 0.27 Acbd6 acyl-Coenzyme A binding domain containing 6 4.29 5.19 0.27 Wwc1 WW, C2 and coiled-coil domain containing 1 6.58 7.44 0.28 Dfna5 h deafness, autosomal dominant 5 homolog (human) 3.38 3.26 0.29 Sall3 sal-like 3 (Drosophila) 3.22 3.55 0.29 LOC667668 Hypothetical protein LOC667668 4.88 9.05 0.29 Abcb4 ATP-binding cassette, sub-family B (MDR/TAP), member 4 3.28 4.29 0.30 Pygm muscle glycogen phosphorylase 4.52 4.07 0.30 Rdh9 retinol dehydrogenase 9 7.88 3.44 0.30 Ppm1j protein phosphatase 1J 2.59 3.99 0.30 Gpr120 G protein-coupled receptor 120 3.39 2.61 0.30 A930018M24Rik RIKEN cDNA A930018M24 gene 7.15 26.90 0.30 Pctk2 PCTAIRE-motif protein kinase 2 4.81 3.48 0.31 Clpb ClpB caseinolytic peptidase B homolog (E. coli) 3.11 4.16 0.32 Dusp23 dual specificity phosphatase 23 3.33 4.45 0.33 Osgep O-sialoglycoprotein endopeptidase 2.37 3.47 0.33 Plec1 plectin 1 4.24 4.82 0.33 7530404M11Rik RIKEN cDNA 7530404M11 gene 4.55 5.24 0.34

Jia et al. www.pnas.org/cgi/content/short/0902425106 4of10 RorbϪ/Ϫ;CrxpNrl Gene Symbol Gene Name RorbϪ/Ϫ vs WT NrlϪ/Ϫ vs WT to RorbϪ/Ϫ (ratio)

A930009A15Rik RIKEN cDNA A930009A15 gene 16.66 18.53 0.36 Igsf3 immunoglobulin superfamily, member 3 5.09 3.24 0.36 Six6os1 Six6 opposite strand transcript 1 2.60 2.94 0.37 Gnb3 guanine nucleotide binding protein, beta 3 2.89 4.23 0.37 Eif3 s9 eukaryotic translation initiation factor 3, subunit 9 (eta) 2.84 2.94 0.38 2310026E23Rik RIKEN cDNA 2310026E23 gene 4.00 4.24 0.38 Elk3 ELK3, member of ETS oncogene family 7.61 5.82 0.39 A730062M13Rik RIKEN cDNA A730062M13 gene 5.88 4.80 0.39 D230010M03Rik RIKEN cDNA D230010M03 gene 2.58 3.92 0.40 Epha10 Eph receptor A10 3.36 3.51 0.40 Crot carnitine O-octanoyltransferase 3.10 2.97 0.40 0610037M15Rik RIKEN cDNA 0610037M15 gene 5.02 4.10 0.42 Prmt8 protein arginine N-methyltransferase 8 3.28 2.87 0.44 Nfkb1 nuclear factor of kappa light chain gene enhancer in B-cells 1, 3.48 3.41 0.45 p105 Cltb clathrin, light polypeptide (Lcb) 3.07 3.60 0.47 Rxrg retinoid X receptor gamma 4.50 6.37 0.49 St3 gal3 ST3 beta-galactoside alpha-2,3-sialyltransferase 3 2.83 3.34 0.49 IMAGE:30247174 CDNA clone IMAGE:30247174 3.00 5.00 0.49 Mtap6 microtubule-associated protein 6 2.86 2.78 0.51 Pnp /// LOC545044 purine-nucleoside phosphorylase /// similar to 2.33 5.79 0.51 purine-nucleoside phosphorylase /// similar to purine-nucleoside phosphorylase Pnp purine-nucleoside phosphorylase 2.45 5.21 0.52 C130076O07Rik RIKEN cDNA C130076O07 gene 3.07 3.33 0.54 6330512M04Rik RIKEN cDNA 6330512M04 gene 3.23 3.49 0.54 Cabp5 calcium binding protein 5 2.46 2.99 0.54 Gem GTP binding protein (gene overexpressed in skeletal muscle) 2.79 3.55 0.55 Tmem158 transmembrane protein 158 3.02 6.17 0.56 4930544G21Rik RIKEN cDNA 4930544G21 gene 2.27 2.71 0.56 Scg3 secretogranin III 2.62 2.21 0.58 Prtg protogenin homolog (Gallus gallus) 4.64 3.56 0.60 Jam3 junction adhesion molecule 3 3.36 4.02 0.61 Rbp4 retinol binding protein 4, plasma 2.95 3.30 0.62 9330159M07Rik RIKEN cDNA 9330159M07 gene 4.38 4.73 0.64 Smpdl3a sphingomyelin phosphodiesterase, acid-like 3A 4.12 5.63 0.66 Cxx1c CAAX box 1 homolog C (human) 3.10 3.83 0.67 E030004N02Rik RIKEN cDNA E030004N02 gene 3.61 2.93 0.69 1700012D01Rik RIKEN cDNA 1700012D01 gene 4.16 2.74 0.70 Ptpn13 protein tyrosine phosphatase, non-receptor type 13 3.52 3.33 0.76 Six6 sine oculis-related homeobox 6 homolog (Drosophila) 2.75 3.37 0.79 Sgce sarcoglycan, epsilon 2.77 2.81 0.80 Ampd2 adenosine monophosphate deaminase 2 (isoform L) 2.50 3.00 0.84 Klf3 Kruppel-like factor 3 (basic) 2.65 2.82 0.93 Pla2r1 phospholipase A2 receptor 1 Ϫ2.78 Ϫ2.54 0.48 Arg2 arginase type II Ϫ5.79 Ϫ4.98 0.61 2610034M16Rik RIKEN cDNA 2610034M16 gene Ϫ14.47 Ϫ11.04 0.67 Hcls1 hematopoietic cell speciﬁc Lyn substrate 1 Ϫ6.91 Ϫ3.67 0.70 Gas7 growth arrest speciﬁc 7 Ϫ4.14 Ϫ3.03 0.72 Slco4a1 solute carrier organic anion transporter family, member 4a1 Ϫ3.81 Ϫ3.58 0.72 Agpat3 1-acylglycerol-3-phosphate O-acyltransferase 3 Ϫ5.30 Ϫ2.75 0.73 Ppap2c phosphatidic acid phosphatase type 2c Ϫ6.81 Ϫ5.54 0.82 Adipor1 adiponectin receptor 1 Ϫ2.84 Ϫ3.57 0.83 St3 gal1 ST3 beta-galactoside alpha-2,3-sialyltransferase 1 Ϫ3.27 Ϫ3.68 0.89 St8 sia1 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1 Ϫ3.30 Ϫ4.18 0.94 Rdh12 retinol dehydrogenase 12 Ϫ6.17 Ϫ4.59 0.95 Ccdc126 coiled-coil domain containing 126 Ϫ3.43 Ϫ2.70 0.96 Grtp1 GH regulated TBC protein 1 Ϫ4.06 Ϫ3.07 0.96 Samd7 sterile alpha motif domain containing 7 Ϫ3.45 Ϫ4.91 0.96 Rom1 rod outer segment membrane protein 1 Ϫ3.76 Ϫ3.35 0.97 2810030D12Rik RIKEN cDNA 2810030D12 gene Ϫ7.44 Ϫ3.43 0.98 Plekhf2 pleckstrin homology domain containing, family F (with FYVE Ϫ7.18 Ϫ5.19 0.99 domain) member 2 Ibrdc2 IBR domain containing 2 Ϫ5.72 Ϫ4.74 1.00

Jia et al. www.pnas.org/cgi/content/short/0902425106 5of10 RorbϪ/Ϫ;CrxpNrl Gene Symbol Gene Name RorbϪ/Ϫ vs WT NrlϪ/Ϫ vs WT to RorbϪ/Ϫ (ratio)

C430045I18Rik RIKEN cDNA C430045I18 gene Ϫ2.64 Ϫ2.73 1.02 Dhh desert hedgehog Ϫ5.90 Ϫ2.97 1.04 Tdrd7 tudor domain containing 7 Ϫ2.86 Ϫ4.62 1.04 D6Wsu176e DNA segment, Chr 6, Wayne State University 176, expressed Ϫ3.18 Ϫ2.82 1.05 Akp2 alkaline phosphatase 2, liver Ϫ4.45 Ϫ3.64 1.06 Tnfaip3 tumor necrosis factor, alpha-induced protein 3 Ϫ7.61 Ϫ8.68 1.07 Sh2d1a SH2 domain protein 1A Ϫ31.98 Ϫ15.83 1.07 Esrrb estrogen related receptor, beta Ϫ7.74 Ϫ25.66 1.08 Ap2a2 adaptor protein complex AP-2, alpha 2 subunit Ϫ2.78 Ϫ2.70 1.08 Optn optineurin Ϫ3.56 Ϫ3.73 1.10 Plk1 polo-like kinase 1 (Drosophila) Ϫ3.20 Ϫ4.11 1.11 Ppp3cc protein phosphatase 3, catalytic subunit, gamma isoform Ϫ3.04 Ϫ3.11 1.11 Dusp14 dual specificity phosphatase 14 Ϫ3.88 Ϫ3.14 1.14 Arfl4 ADP-ribosylation factor 4-like Ϫ3.24 Ϫ4.16 1.16 ORF28 open reading frame 28 Ϫ2.25 Ϫ2.57 1.18 Taok3 TAO kinase 3 Ϫ2.50 Ϫ3.19 1.19 4933429D07Rik RIKEN cDNA 4933429D07 gene Ϫ5.39 Ϫ3.11 1.20 Arl13b ADP-ribosylation factor-like 13B Ϫ3.02 Ϫ3.39 1.20 A330094K24Rik RIKEN cDNA A330094K24 gene Ϫ7.92 Ϫ5.92 1.25 D1Ertd622e DNA segment, Chr 1, ERATO Doi 622, expressed Ϫ3.70 Ϫ3.68 1.28 Sap30 sin3 associated polypeptide Ϫ2.48 Ϫ3.52 1.30 Fscn2 fascin homolog 2, actin-bundling protein, retinal Ϫ32.47 Ϫ12.95 1.30 Thoc5 THO complex 5 Ϫ3.00 Ϫ3.47 1.30 Zfp472 zinc finger protein 472 Ϫ2.42 Ϫ2.78 1.30 Glt28d2 glycosyltransferase 28 domain containing 2 Ϫ5.15 Ϫ4.21 1.31 Hspa1b heat shock protein 1B Ϫ3.10 Ϫ4.34 1.36 Lmo1 LIM domain only 1 Ϫ5.89 Ϫ5.11 1.36 Gadd45a growth arrest and DNA-damage-inducible 45 alpha Ϫ3.05 Ϫ3.11 1.38 B4 galt1 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, Ϫ2.77 Ϫ2.94 1.38 polypeptide 1 2810439F02Rik RIKEN cDNA 2810439F02 gene Ϫ3.16 Ϫ2.89 1.38 1500016O10Rik RIKEN cDNA 1500016O10 gene Ϫ3.90 Ϫ2.72 1.39 Pitpnm3 PITPNM family member 3 Ϫ2.66 Ϫ3.24 1.40 Pde6a phosphodiesterase 6A, cGMP-specific, rod, alpha Ϫ6.57 Ϫ6.44 1.40 Pdia5 protein disulfide isomerase associated 5 Ϫ8.77 Ϫ9.92 1.42 Lrrc2 leucine rich repeat containing 2 Ϫ4.54 Ϫ7.78 1.43 Faim Fas apoptotic inhibitory molecule Ϫ8.35 Ϫ6.18 1.43 Csda cold shock domain protein A Ϫ3.30 Ϫ2.87 1.44 Ext1 exostoses (multiple) 1 Ϫ3.81 Ϫ3.65 1.45 Mlf1 myeloid leukemia factor 1 Ϫ3.71 Ϫ7.21 1.50 Rnf207 ring finger protein 207 Ϫ11.19 Ϫ9.57 1.51 9930021J17Rik RIKEN cDNA 9930021J17 gene Ϫ6.61 Ϫ7.38 1.53 Zfyve28 Zinc finger, FYVE domain containing 28 Ϫ7.42 Ϫ5.25 1.53 Taf4b TAF4B RNA polymerase II, TATA box binding protein Ϫ4.92 Ϫ4.02 1.54 (TBP)-associated factor Tmem108 transmembrane protein 108 Ϫ3.61 Ϫ3.19 1.60 Dhrs3 dehydrogenase/reductase (SDR family) member 3 Ϫ2.56 Ϫ4.04 1.61 Dleu7 deleted in lymphocytic leukemia, 7 Ϫ3.98 Ϫ7.38 1.62 Ric8b resistance to inhibitors of cholinesterase 8 homolog B (C. Ϫ3.68 Ϫ4.70 1.63 elegans) Marveld3 MARVEL (membrane-associating) domain containing 3 Ϫ5.43 Ϫ5.58 1.70 Gpsm2 G-protein signalling modulator 2 (AGS3-like, C. elegans) Ϫ8.41 Ϫ6.98 1.70 Dpf3 D4, zinc and double PHD fingers, family 3 Ϫ5.36 Ϫ5.00 1.71 Polg2 polymerase (DNA directed), gamma 2, accessory subunit Ϫ6.04 Ϫ8.58 1.79 Cdr2 cerebellar degeneration-related 2 Ϫ11.26 Ϫ8.89 1.81 Wisp1 WNT1 inducible signaling pathway protein 1 Ϫ23.07 Ϫ21.31 1.83 Spata1 spermatogenesis associated 1 Ϫ5.69 Ϫ5.56 1.85 Col19a1 procollagen, type XIX, alpha 1 Ϫ5.87 Ϫ6.71 1.86 C730048C13Rik RIKEN cDNA C730048C13 gene Ϫ17.86 Ϫ42.10 1.90 5830408C22Rik RIKEN cDNA 5830408C22 gene Ϫ2.96 Ϫ3.26 1.91 Ndrl N-myc downstream regulated-like Ϫ2.74 Ϫ3.34 1.96 Aqp1 aquaporin 1 Ϫ6.59 Ϫ30.92 1.99 Npal1 NIPA-like domain containing 1 Ϫ7.32 Ϫ7.97 2.09 Stk17b serine/threonine kinase 17b (apoptosis-inducing) Ϫ7.17 Ϫ6.64 2.13

Jia et al. www.pnas.org/cgi/content/short/0902425106 6of10 RorbϪ/Ϫ;CrxpNrl Gene Symbol Gene Name RorbϪ/Ϫ vs WT NrlϪ/Ϫ vs WT to RorbϪ/Ϫ (ratio)

Txnl6 thioredoxin-like 6 Ϫ8.21 Ϫ3.96 2.14 Mef2c myocyte enhancer factor 2C Ϫ12.45 Ϫ12.14 2.15 Gnb1 guanine nucleotide binding protein, beta 1 Ϫ10.95 Ϫ48.90 2.20 BC038479 cDNA sequence BC038479 Ϫ16.25 Ϫ22.91 2.21 Plekha2 pleckstrin homology domain-containing, family A Ϫ5.18 Ϫ11.09 2.26 (phosphoinositide binding speciﬁc) member 2 Vax2os1 Vax2 opposite strand transcript 1 Ϫ11.43 Ϫ11.27 2.27 Susd3 sushi domain containing 3 Ϫ14.21 Ϫ17.65 2.27 Guca1b guanylate cyclase activator 1B Ϫ18.90 Ϫ8.93 2.35 Nrl neural retina leucine zipper gene Ϫ13.28 Ϫ480.88 2.46 BC016201 cDNA sequence BC016201 Ϫ13.31 Ϫ36.89 2.46 Ebpl emopamil binding protein-like Ϫ4.75 Ϫ8.08 2.47 Gnat1 guanine nucleotide binding protein, alpha transducing 1 Ϫ5.66 Ϫ712.64 2.48 Reep6 receptor accessory protein 6 Ϫ15.59 Ϫ22.14 2.68 A930036K24Rik RIKEN cDNA A930036K24 gene Ϫ23.16 Ϫ55.71 3.03 Slc24a1 solute carrier family 24 (sodium/potassium/calcium exchanger), Ϫ16.51 Ϫ46.44 3.08 member 1 Samd11 sterile alpha motif domain containing 11 Ϫ14.78 Ϫ17.94 3.19 Kcnj14 potassium inwardly-rectifying channel, subfamily J, member 14 Ϫ32.29 Ϫ86.43 3.33 Cnga1 cyclic nucleotide gated channel alpha 1 Ϫ19.77 Ϫ266.08 3.61 Glb1l3 galactosidase, beta 1 like 3 Ϫ6.41 Ϫ7.13 3.74 Abca13 /// LOC672028 ATP-binding cassette, sub-family A (ABC1), member 13 /// Ϫ8.81 Ϫ17.07 3.77 similar to ATP binding cassette, sub-family A (ABC1), member 13 Nr2e3 nuclear receptor subfamily 2, group E, member 3 Ϫ18.02 Ϫ100.96 3.86 LOC672028 similar to ATP binding cassette, sub-family A (ABC1), Ϫ11.44 Ϫ13.65 4.50 member 13 Pde6b phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide Ϫ24.45 Ϫ19.24 4.54 Rho rhodopsin Ϫ18.38 Ϫ278.45 6.22

Jia et al. www.pnas.org/cgi/content/short/0902425106 7of10 Table S3. In situ hybridization probes Gene Name Accession # Coordinates, nt Size, bp Vector mS opsin AF190670 269–887 618 pGEM-TEZ mM opsin NM_008106 32–705 673 pGEM-TEZ mRhodopsin NM_145383 27–327 300 pGEMT hNr2e3 NM_013708 196–1383 1200 pGEM-11zf(-) hNrl BC012395 159–1158 1000 pGEM-11zf(-) mCrx NM_007770 119–1015 896 pGEM-TEZ mOtx2 NM_144841 408–1108 701 pCRII mPde6a NM_146086 107–954 847 pCRII mGnat1 NM_008140 45–1097 1054 pCRII mGnat2 NM_008141 82–889 807 pCRII mArr3 AF156979 435–1194 760 pCRII

Jia et al. www.pnas.org/cgi/content/short/0902425106 8of10 Table S4. Antibodies for Western blot and immunostaining on tissues Antibody Species Working Conc. Source

Nrl Rabbit polyclonal 1:10,000 Swaroop A., NEI Nr2e3 Rabbit polyclonal 1:500 Swaroop A., NEI Rhodopsin Mouse monoclonal 1:1000 Chemicon MAb5316 Gnat1 Rabbit polyclonal 1:10,000 Abcam ab19427 Pde6a Rabbit polyclonal 1:5000 Abcam ab5659 Gnb1 (C-16) Rabbit polyclonal 1:500 Santa Cruz Biotechnology sc-379 Opn1 sw (N-20) Goat polyclonal 1:250 Santa Cruz Biotechnology sc-14363 Ror␤ Rabbit polyclonal 1:2500 Diagenode pAb-RORbHS-100 ␤Gal Mouse monoclonal 1:200 Promega Z378A Active Caspase3 Rabbit polyclonal 1:250 Promega G748 Actin Mouse monoclonal 1:5000 Chemicon MAb1501 Trb2 Rabbit polyclonal 1:2500 Ref. 1 Crx Rabbit polyclonal 1:4000 Described in the present study

1. Ng L, Ma M, Curran T, and Forrest D (2009). Developmental expression of thyroid hormone receptor beta2 protein in cone photoreceptors in the mouse. Neuroreport 20:627–631.

Jia et al. www.pnas.org/cgi/content/short/0902425106 9of10 Table S5. Primers for real time qPCR Gene Name Genbank# Amplicon Size (bp) Forward Primer Reverse Primer

Rho NM_145383 139 CCCTTCTCCAACGTCACAGG TGAGGAAGTTGATGGGGAAGC Pde6b NM_008806 136 GCAGCACTTTTTGAACTGGTG CATTGCGCTGGCGGTACATA Cnga1 NM_007723 116 AATACGTGGCATTCCTTCGTAAA GAGCCATTGTCATCGTCAGAAA Nr2e3 NM_013708 146 TGTGCAGAATGAGCGCCAA TTGCAGACACAGACGTGGG Nrl NM_008736 120 TCACCCACCTTCAGTGAGC CCCGAGAACCTCATCCGAC Gnat1 NM_008140 103 GATGCCCGCACTGTGAAAC CCAGCGAATACCCGTCCTG Opn1mw NM_008106 162 TCGAAACTGCATCTTACATCTC GGAGGTAAAACATGGCCAAA Opn1 sw AF190670 176 TGCTGGGGATCTGAGATGAT AATGAGGTGAGGCCATTCTG Arr3 NM_133205 230 CCCTCACAGCCTTACAGGAG CTGCACTTTCCGTACAACCAG Gnat2 NM_008141 115 GGATGGCTACTCACCCGAAG TGCATAGTCAATGCCTAGTGTG Slc24a1 NM_144813 136 GGAGAGGCGGTTACTCCGA GGAGACCTTTGTCCACATTGAG Rdh12 AK020927 76 ATCTTGGTACTGCTTACGTCCT CACCAGCAAAGAACTTCCTGA Rom1 NM_009073 154 CTCCAACCCCGTATCCGTTTG GAGCAGGGAATGAACAAGAGG Rp1 h NM_011283 108 CCTGTAGTGGCTAAACGCATC CAGCAGAGCGTCAAAAGTCTTA Gngt1 NM_010314 205 TCAACATCGAAGACCTGACAGA ACACAGCCTCCTTTGAGTTCC Rgs9bp NM_145840 146 CAGGTGGGCGAGATGATTGAC CGCTCCTCTACCGAAATGC Pias3 NM_018812 296 GAAGGAGGCATCAGAGGTTTG TAGACAGGAAATCACTGCCCA Pcdh15 NM_023115 106 CTGGGGCCAGTATGACGATG TGTACCGTTTCGACTCTCTTCA Elovl2 NM_019423 100 CCTGCTCTCGATATGGCTGG AAGAAGTGTGATTGCGAGGTTAT Gnb3 NM_013530 118 AAGAAGCAGATTGCTGATGCC GTCCCCTTAATGTCCTCCGTG Pde6 h NM_023898 126 AGGGGTGAAAGGGTTTGGAGA ATGATCCCGAACTGAGCAAGC Rxrg NM_009107 130 CATGAGCCCTTCAGTAGCCTT CGGAGAGCCAAGAGCATTGAG Gngt2 NM_023121 128 CAGGACCTCAGTGAGAAGGAG CCTGCTTGGGCCTCTACATAAT Crx NM_007770 160 GTTCAAGAATCGTAGGGCGAA TGAGATGCCCAAAGGATCTGT Thrb2 NM_009380.3 208 CCTGTAGTTACCCTGGAAACCTG TACCCTGTGGCTTTGTCCC Actb NM_007393.3 222 TGCTGTCCCTGTATGCCTCTG TTGATGTCACGCACGATTTCC

Most primer sequences for quantitative PCR analysis were given by Primer Bank (http://pga.mgh.harvard.edu/primerbank).

Jia et al. www.pnas.org/cgi/content/short/0902425106 10 of 10