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ZFIN The Zebrafish Information Network
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About ZFIN
The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the
zebrafish (Danio rerio) as a model organism. ZFIN provides a wide array of expertly curated,
organized and cross-referenced zebrafish research data.
Learn More
New Data in ZFIN
FIGURE 3 of van der Veen et al., 2026
The spatiotemporal overview of retinoschisin (Rs1) protein presence during the first five days of retinal development shows that Rs1 protein presence is first detected at 48 hpf and increases in intensity and spatial distribution up to 120 hpf. Cryosections were incubated with primary antibodies overnight at 4°C. At least 3 biological replicates were examined per timepoint. A: No positive immunostaining of Rs1 was observed within the first 24 h of retinal development. B: At 48 h, Rs1 protein presence was first observed in this experiment in low levels in the ganglion cell layer (GCL). C: At 60 hpf, a weak signal was detected in the GCL, the inner plexiform layer (IPL), and the outer nuclear layer (ONL) D‐E. The intensity of Rs1 immunostaining continued to increase throughout 72 (D), 96 (E), and 120 (F) hpf. G. Co‐staining of Rs1 and cone arrestin (Arr3) demonstrated that Rs1 surrounds the developing outer segments at 120 hpf. F. Rs1 presence was quantified per retinal layer and normalized to total Rs1 signal per sample. Data represent mean percentage of Rs1 signal per layer (± standard error of the mean). A shift in Rs1 localization is observed from predominately INL at 72 hpf toward increasing IPL and GCL contribution at later stages. Hpf = hours post fertilization, Rs1 = retinoschisin, Arr3 = cone arrestin, DAPI = 4′,6‐diamidino‐2‐phenylindole.
FIGURE 7 of van der Veen et al., 2026
Delivery of translation‐blocking morpholino oligos (MO) targeting rs1a and rs1b mRNA results in significant downregulation of visual perception and camera‐type eye development at 96 h post‐fertilization (hpf), as well as impaired photoreceptor development. Following RNA sequencing, gene ontology (GO) enrichment analyses were performed. A: All significantly downregulated GO terms for biological processes (BP; blue bars) and molecular function (MF; red bars). No terms for cellular components were significantly enriched in differentially expressed genes (DEGs). n refers to the number of DEGs mapped to the term. B: All upregulated GO terms for cellular components (CC; green bars). MF and BP did not yield terms significantly enriched in DEGs. n refers to the number of DEGs mapped to the term. C: Heatmap of phototransduction‐related genes (derived from Kyoto Encyclopedia of Genes and Genomes [KEGG] pathway). Red and green colors indicate respectively down‐ and upregulation of the genes in MO compared to scrambled (SC). The scale ranges from strongly downregulated (fold change 0.18) to slightly upregulated (fold change 2.0). D: Immunofluorescent staining of blue cone pigment small‐wavelength sensitive opsin (OPN1SW) in 4 and 5 day‐old SC‐ and MO‐injected zebrafish. Padj = adjusted p‐value. Dpf = days post‐fertilization.
Fig. 4 of Pan et al., 2025
A Phex expression at different stages post-fertilization in zebrafish (n = 20 embryos per time point, 3 independent experiments). B Validation of Phex expression inhibition efficiency (n = 15 embryos per group, 3 independent experiments). C Statistics depicting mortality and malformation rates at varying concentrations of MO (n = 120 embryos total, pooled from 3 independent experiments with n = 40 per experiment). D Microinjection of zebrafish eggs and observation of tooth development at 6 days post-fertilization (dpf) via Alizarin Red staining (n = 30 embryos per group, 3 independent experiments). Scale bars: 250 μm (embryo images), 100 μm (tooth staining images). Data represent mean ± SEM. Statistical analysis performed using Student’s t-test for pairwise comparisons and one-way ANOVA for multiple group comparisons. *p < 0.05, **p < 0.01, ***p < 0.001 vs. control group
Fig. 2 of Arkush et al., 2025
Zebrafish knockdown modeling and rescue.A In situ hybridization using antibodies for MED17 and MED29 in a zebrafish embryo model, demonstrating restricted brain expression pattern for both. AS – antisense, S – sense. B Immunohistochemistry staining of the zebrafish MED17, MED29, and P53 morphants using PValb7 antibodies directed at the GABAergic Purkinje cerebellar cells and Vglut1a antibodies directed at the Glutamatergic Granule cerebellar cells. Left panels – coronal sections, right panels – sagittal sections. WT – wild type. The arrows signify the location of the midbrain-hindbrain boundary (MHB) from which the cerebellar structures develop. MED17 and MED29 Morphants exhibit prominent reduced staining of GABAergic Purkinje neurons, but a much lesser reduction in staining of glutamatergic granule neurons. C Quantitative analysis of the relative expression GABAergic Purkinje cerebellar cells (on the left) and Glutamatergic Granule cerebellar cells (on the right) in the wt, and MED29 and MED17 morphants, by measuring mRNA levels of prototypical genes by rtPCR. A significant reduction of the expression of genes typical to Purkinje cells is seen in both MED29 and MED17 morphants, however, there is no reduction in the expression of genes typical to Granules cells. D Examples of immunohistochemistry with PValb7 staining, demonstrating normal cerebellar expression in the un-injected (UI) control larvae (left image), absent cerebellar expression in the MED29 morphant (second from left), and varying degrees of increasing cerebellar expression designated as weak and strong (two panels on the right) following rescue with a plasmid containing human wt MED29. E Quantitative analysis of the relative expression of pvalb7 gene typical for GABAergic Purkinje cerebellar cells (measured by rtPCR), show normal levels in the wt control larva (left), significantly decreased levels in the MED29 morphant (middle), and an increase in expression in the MED29 morphant following rescue with a human wt MED29, to levels that are not significantly different from the control wt. F Statistical analysis of the proportion of larvae demonstrating a positive touch response in the MED29 morphants (top bar) and MED29 morphants following rescue with plasmids containing human wt MED29 in low concentrations of 5 ng/μl (middle bar) and higher concentrations of 10 ng/μl (bottom bar), showing significantly increased fraction of larva demonstrating positive touch response following rescue with a high concentration but not a low concentration. G Statistical analysis of the proportion of larvae demonstrating a “strong” cerebellar expression (indicated by pvalb7 staining as shown in D among the MED29 morphants (top bar) and MED29 morphants following rescue with plasmids containing human wt MED29 in low concentrations of 5 ng/μl (middle bar) and higher concentrations of 10 ng/μl (bottom bar), showing significantly increased fraction of larva with strong cerebellar expression following rescue with a high concentration but not a low concentration.
Fig. 2 of Gupta et al., 2025
Srrm4 is expressed in proliferating notch1a and differentiated elavl3 neurons during early brain development. a–d) Partial (20 μm depth) maximum intensity projections of srrm4 mRNA expression at 24 and 48 hpf. Dorsal view in (a) and sagittal view in (b) at 24 hpf. Dorsal view in (c) and sagittal view in (d) at 48 hpf. Anterior is to the left. Scale bars = 100 μm. e–e″) Single plane image of Mo of srrm4 co-labeled with notch1a mRNA at 48 hpf. e) srrm4 expression. e′) notch1a expression. e″) srrm4 and notch1a merged images. f–f″) Single plane image of Mo of srrm4 co-labeled with elavl3 mRNA at 48 hpf. f) srrm4 expression. f′) elavl3 expression. f″) srrm4 and elavl3 merged images. Areas of overlap, which appear yellow, indicate presumed co-localization. Scale bars = 50 μm. Cb, cerebellum; Di, diencephalon; Mo, medulla oblongata; Oe, olfactory epithelium; Ot, optic tectum; Te, telencephalon.
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About ZFIN
The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the
zebrafish (Danio rerio) as a model organism. ZFIN provides a wide array of expertly curated,
organized and cross-referenced zebrafish research data.
Learn More
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FIGURE 3 of van der Veen et al., 2026
The spatiotemporal overview of retinoschisin (Rs1) protein presence during the first five days of retinal development shows that Rs1 protein presence is first detected at 48 hpf and increases in intensity and spatial distribution up to 120 hpf. Cryosections were incubated with primary antibodies overnight at 4°C. At least 3 biological replicates were examined per timepoint. A: No positive immunostaining of Rs1 was observed within the first 24 h of retinal development. B: At 48 h, Rs1 protein presence was first observed in this experiment in low levels in the ganglion cell layer (GCL). C: At 60 hpf, a weak signal was detected in the GCL, the inner plexiform layer (IPL), and the outer nuclear layer (ONL) D‐E. The intensity of Rs1 immunostaining continued to increase throughout 72 (D), 96 (E), and 120 (F) hpf. G. Co‐staining of Rs1 and cone arrestin (Arr3) demonstrated that Rs1 surrounds the developing outer segments at 120 hpf. F. Rs1 presence was quantified per retinal layer and normalized to total Rs1 signal per sample. Data represent mean percentage of Rs1 signal per layer (± standard error of the mean). A shift in Rs1 localization is observed from predominately INL at 72 hpf toward increasing IPL and GCL contribution at later stages. Hpf = hours post fertilization, Rs1 = retinoschisin, Arr3 = cone arrestin, DAPI = 4′,6‐diamidino‐2‐phenylindole.
FIGURE 7 of van der Veen et al., 2026
Delivery of translation‐blocking morpholino oligos (MO) targeting rs1a and rs1b mRNA results in significant downregulation of visual perception and camera‐type eye development at 96 h post‐fertilization (hpf), as well as impaired photoreceptor development. Following RNA sequencing, gene ontology (GO) enrichment analyses were performed. A: All significantly downregulated GO terms for biological processes (BP; blue bars) and molecular function (MF; red bars). No terms for cellular components were significantly enriched in differentially expressed genes (DEGs). n refers to the number of DEGs mapped to the term. B: All upregulated GO terms for cellular components (CC; green bars). MF and BP did not yield terms significantly enriched in DEGs. n refers to the number of DEGs mapped to the term. C: Heatmap of phototransduction‐related genes (derived from Kyoto Encyclopedia of Genes and Genomes [KEGG] pathway). Red and green colors indicate respectively down‐ and upregulation of the genes in MO compared to scrambled (SC). The scale ranges from strongly downregulated (fold change 0.18) to slightly upregulated (fold change 2.0). D: Immunofluorescent staining of blue cone pigment small‐wavelength sensitive opsin (OPN1SW) in 4 and 5 day‐old SC‐ and MO‐injected zebrafish. Padj = adjusted p‐value. Dpf = days post‐fertilization.
Fig. 4 of Pan et al., 2025
A Phex expression at different stages post-fertilization in zebrafish (n = 20 embryos per time point, 3 independent experiments). B Validation of Phex expression inhibition efficiency (n = 15 embryos per group, 3 independent experiments). C Statistics depicting mortality and malformation rates at varying concentrations of MO (n = 120 embryos total, pooled from 3 independent experiments with n = 40 per experiment). D Microinjection of zebrafish eggs and observation of tooth development at 6 days post-fertilization (dpf) via Alizarin Red staining (n = 30 embryos per group, 3 independent experiments). Scale bars: 250 μm (embryo images), 100 μm (tooth staining images). Data represent mean ± SEM. Statistical analysis performed using Student’s t-test for pairwise comparisons and one-way ANOVA for multiple group comparisons. *p < 0.05, **p < 0.01, ***p < 0.001 vs. control group
Fig. 2 of Arkush et al., 2025
Zebrafish knockdown modeling and rescue.A In situ hybridization using antibodies for MED17 and MED29 in a zebrafish embryo model, demonstrating restricted brain expression pattern for both. AS – antisense, S – sense. B Immunohistochemistry staining of the zebrafish MED17, MED29, and P53 morphants using PValb7 antibodies directed at the GABAergic Purkinje cerebellar cells and Vglut1a antibodies directed at the Glutamatergic Granule cerebellar cells. Left panels – coronal sections, right panels – sagittal sections. WT – wild type. The arrows signify the location of the midbrain-hindbrain boundary (MHB) from which the cerebellar structures develop. MED17 and MED29 Morphants exhibit prominent reduced staining of GABAergic Purkinje neurons, but a much lesser reduction in staining of glutamatergic granule neurons. C Quantitative analysis of the relative expression GABAergic Purkinje cerebellar cells (on the left) and Glutamatergic Granule cerebellar cells (on the right) in the wt, and MED29 and MED17 morphants, by measuring mRNA levels of prototypical genes by rtPCR. A significant reduction of the expression of genes typical to Purkinje cells is seen in both MED29 and MED17 morphants, however, there is no reduction in the expression of genes typical to Granules cells. D Examples of immunohistochemistry with PValb7 staining, demonstrating normal cerebellar expression in the un-injected (UI) control larvae (left image), absent cerebellar expression in the MED29 morphant (second from left), and varying degrees of increasing cerebellar expression designated as weak and strong (two panels on the right) following rescue with a plasmid containing human wt MED29. E Quantitative analysis of the relative expression of pvalb7 gene typical for GABAergic Purkinje cerebellar cells (measured by rtPCR), show normal levels in the wt control larva (left), significantly decreased levels in the MED29 morphant (middle), and an increase in expression in the MED29 morphant following rescue with a human wt MED29, to levels that are not significantly different from the control wt. F Statistical analysis of the proportion of larvae demonstrating a positive touch response in the MED29 morphants (top bar) and MED29 morphants following rescue with plasmids containing human wt MED29 in low concentrations of 5 ng/μl (middle bar) and higher concentrations of 10 ng/μl (bottom bar), showing significantly increased fraction of larva demonstrating positive touch response following rescue with a high concentration but not a low concentration. G Statistical analysis of the proportion of larvae demonstrating a “strong” cerebellar expression (indicated by pvalb7 staining as shown in D among the MED29 morphants (top bar) and MED29 morphants following rescue with plasmids containing human wt MED29 in low concentrations of 5 ng/μl (middle bar) and higher concentrations of 10 ng/μl (bottom bar), showing significantly increased fraction of larva with strong cerebellar expression following rescue with a high concentration but not a low concentration.
Fig. 2 of Gupta et al., 2025
Srrm4 is expressed in proliferating notch1a and differentiated elavl3 neurons during early brain development. a–d) Partial (20 μm depth) maximum intensity projections of srrm4 mRNA expression at 24 and 48 hpf. Dorsal view in (a) and sagittal view in (b) at 24 hpf. Dorsal view in (c) and sagittal view in (d) at 48 hpf. Anterior is to the left. Scale bars = 100 μm. e–e″) Single plane image of Mo of srrm4 co-labeled with notch1a mRNA at 48 hpf. e) srrm4 expression. e′) notch1a expression. e″) srrm4 and notch1a merged images. f–f″) Single plane image of Mo of srrm4 co-labeled with elavl3 mRNA at 48 hpf. f) srrm4 expression. f′) elavl3 expression. f″) srrm4 and elavl3 merged images. Areas of overlap, which appear yellow, indicate presumed co-localization. Scale bars = 50 μm. Cb, cerebellum; Di, diencephalon; Mo, medulla oblongata; Oe, olfactory epithelium; Ot, optic tectum; Te, telencephalon.
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