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. 2021 Aug 30;11:17340. doi: 10.1038/s41598-021-96837-z

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Transcriptome profiles of adult zebrafish photoreceptor subtypes. (A) Schematic representation of the major cell classes in the zebrafish retina based on a prior design⁷. Photoreceptor cell types and ON and OFF bipolar cells are highlighted in color, whereas other retinal cell types are in grey. The ON bipolar cell cluster in our single cell data expresses genes specific to both rod ON bipolar cells (prkcaa) and cone ON bipolar cells (gnao1b, gnb3a, trpm1a, rgs11, and isl1). See also Fig. S1. ONL outer nuclear layer, INL inner nuclear layer, GCL ganglion cell layer. (B) Isolation of rod and cone cells from transgenic adult zebrafish expressing green fluorescent protein (GFP). GFP-positive cells were collected from each line. A small percentage of GFP-negative cells was also included in the analysis. (C) Automatic clustering of single-cell expression profiles reveals six distinct photoreceptor populations. The plot shows a two-dimensional representation (UMAP) of global gene expression relationships among 2186 cells. (D) Heatmap showing top five differentially enriched genes for each cell population (rows). Columns correspond to single cells grouped by cell cluster. Each cell cluster is colored as in panel (C). Values are row-wise Z-scored gene-expression values. See also Fig. S1A. Full list of differentially enriched genes is provided in Supplementary Data S1.