Figure 1  Cone-Specific and Cone-Enriched Genes Evaluated in the rd7 Mutant by Microarray and In Situ Hybridization
The color coding of text in the column “Gene Name” is as follows: light blue (G1–G15), genes previously reported in the literature to have cone-specific or cone-enriched patterns of expression; yellow (G16–G25), novel cone genes identified in an unrelated study (unpublished data); dark green (G26–G36), novel cone genes identified in the present study that were up-regulated in rd7; light green (G37–G46), additional genes found to be up-regulated in rd7 by microarray in the present study but that had either weak or inapparent cone-specific signal on in situ hybridization; white (G47–G53), additional genes up-regulated by microarray at two different timepoints but with either unusual expression patterns or nonconfirmatory in situ hybridizations. The column “ID” contains identifiers used in the present paper to refer to specific genes. “GenBank ID” contains the GenBank accession number of the clone used to make the probe for in situ hybridization. Within this column, “lab clone” indicates that the probe used for in situ hybridization derived from a clone in our laboratory. The region of the gene to which it corresponds is indicated in Table S1. Columns “P0” through “P21” contain the results of microarray experiments at the given postnatal dates. P0, P6, and P14 time points represent analyses on cDNA microarrays; the P21 time point represents data from an Affymetrix microarray (mouse genome 432 2.0). A red cell with a single up arrow indicates that the gene in question was up-regulated in three out of three microarrays at that time point (as described in Materials and Methods). Those cells labeled orange with a single up arrow and asterisk indicate that the gene in question was up-regulated in two out of three microarrays at that time point. The column “In Situ” lists the type of derepression seen for the gene in question in the rd7 mutant retina (type I and type II are described in the main text). Genes designated “unclassified” represent patterns of derepression that were difficult to classify as either type I or type II (see main text for more details). “Wild type” in this column indicates that the in situ hybridization pattern in the rd7 mutant retina was not different from the wild-type pattern; and “special” indicates a special pattern of expression discussed more fully in the main text. The column “Expression Pattern” contains a concise description of the wild-type expression pattern of the gene in question. In the case of genes for which no signal was obtained on in situ hybridization in the present study, the specified expression pattern derives from reports in the literature. Within this column, “cone > rod” indicates that the gene is expressed in all photoreceptors, but at higher levels in cones than rods; “cone?” indicates very weak staining in a cone-like distribution.
BP, bipolar cells; EP, early photoreceptor expression pattern; IS, inner core segment localization; MG, Müller glia; N/A, not available on the microarray; NS, no signal detected on in situ hybridization; RPE, retinal pigment epithelium.  Nr2e3 expression is first detectable by in situ hybridization around embryonic day 18 (E18); it then peaks around P6 and subsequently decreases to adult levels by P21 (unpublished data).