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Additional Supporting information may be found in the online version of this article.

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DVDY_21988_sm_SuppFigS1.tif7000KSupp. Fig. S1. Spatial expression pattern of selected pineal enriched genes in day 3 zebrafish larvae. In situ hybridization was carried out as described (Toyama and Dawid, 1997). The Affymetrix probe set ID numbers corresponding to the different clones are indicated. A, Dr.9901.1.S1; B, Dr.6401.1.S1; C, Dr.11336.1.A1; D, Dr.9852.1.A1; E and F, Dr.12466.1.A1. F, eyes are removed. All panels show lateral views.
DVDY_21988_sm_SuppFigS2.tif3412KSupp. Fig. S2. GO term analysis of pineal enriched genes selected in Figure 1 at molecular function (MF) level 4. GO terms with P values ≤ 0.1 were selected. Each pie chart represents the results of a different stage (larval or adult) and time (day or night). Each slice indicates the number of genes in a given GO term. The numbers next to the colored squares indicate the order of GO terms arranged by P values (small to large), and correspond to the numbers in parentheses in the table below. The table lists the P values of GO terms in the left column. No entry indicates that the GO term was not enriched in the pineal gland at the given category.
DVDY_21988_sm_SuppFigS3.tif8351KSupp. Fig. S3. GO term analysis of subsets A and C shown in Figure 4 at molecular function (MF) level 3. GO terms with P values ≤ 0.1 were selected. See legend of Supplementary Figure S2 for further explanations.
DVDY_21988_sm_SuppFigS4.tif1213KSupp. Fig. S4. Hierarchical clustering of genes whose expression levels change at night in the pineal gland during development. Genes were selected using the following criteria: average maximum signal ≥200; lowest and highest signal ratio ≥ 3; P value ≤0.05. Low expression, green; high expression, red. Samples were grouped into four subsets, A-D. 1, 3 days; 2, 5 days; 3, 10 days; 4, 3 months; 5, 1-2 years.
DVDY_21988_sm_SuppFigS5.tif9346KSupp. Fig. S5. GO term analysis of subsets A and C shown in Supplementary Figure S4 at biological processes (BP) level 5. See legend of Supplementary Figure S2 for further explanations.
DVDY_21988_sm_SuppFigS6.tif7050KSupp. Fig. S6. GO term analysis of subset A and C shown in Supplementary Figure S4 at molecular function (MF) level 3. See legend of Supplementary Figure S2 for further explanations.
DVDY_21988_sm_SuppTablesS1-S3.xls165KSupp. Table S1. Genes enriched in the larval pineal gland. All genes selected from larval stages in Fig.1 (day non-overlap total: 128; night non-overlap total: 150) are listed. D, genes only in day sample; N, genes only in night sample; DN, genes in both day and night sample. Supp. Table S2. Genes enriched in the adult pineal gland. All genes selected from adult stages in Fig.1 (day non-overlap total: 1018; night non-overlap total: 1017) are listed. D, genes only in day sample; N, genes only in night sample; DN, genes in both day and night sample. Supp. Table S3. Genes highly expressed at night (A) or day (B) in the pineal gland. Samples were analyzed at each developmental stage separately with average minimum signal ≥100 and P value ≤0.05. Probe sets whose fold change between day and night are higher than 1.5 at least in four out of five developmental stages (d3, d5, d10, 3mo, and 1-2 yr) are listed.

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