DOI: 10.5281/zenodo.18677158
title: Müller glia subtypes define neuro-glial associations and spatial morphogen axes in the zebrafish retina

description:  

The code for analysis of these data can be accessed at the following github repository.

These datasets are supplement to the manuscript submission:

Müller glia subtypes define neuro-glial associations and spatial morphogen axes in the zebrafish retina (2026). 

Abstract: Müller glia are instrumental macroglia of the vertebrate retina, once thought to be a homogeneous population. Now Müller glia are generally accepted as transcriptionally heterogeneous, and new evidence suggests functional diversity may exist in the way these cells respond to retinal injury. It remains unclear, however, whether this functional heterogeneity is limited to a transient phenotype that stems from injury or a fundamental feature of the healthy retina. Here, we investigate Müller glia heterogeneity in the uninjured zebrafish retina across development and adulthood using a comprehensive single-cell transcriptomic atlas of the 5 days post-fertilization (dpf) eye, validated in vivo and integrated with 9 dpf and adult datasets. We reveal that Müller glia are partitioned into three constitutive subpopulations that persist from early larval stages into adulthood: 1) a proliferative and immature population in both the peripheral and central retina; 2) a  novel cohort of neuron-associated Müller glia that express coherent transcriptional programs specific to distinct neuronal subtypes, including retinal ganglion, amacrine and horizontal cells; and 3) spatially distinct Müller glia subsets that define a dorso-ventral axis of retinoic acid metabolism, bisected by a novel _cyp26c1_-expressing equatorial domain. Finally, cross-species analysis reveals that while neuron-associated programs are evolutionarily conserved in mammals, the spatial patterning of morphogens in adult retinae may be specific to the teleost lineage. Collectively, these findings provide robust evidence for intrinsic functional heterogeneity in the uninjured vertebrate retina, reframing Müller glia from a general support population to a specialized cellular network that actively maintains retinal geography and function.

Note: The dataset sources from the original authors for Kriukov_2025_human_fetal_mg.h5ad, Li_2024_mouse_mg.h5ad, Li_2026_human_adult_mg.h5ad, Yamagata_2021_chick_mg.h5ad and the 9dpf/adult zebrafish data within the Zebrafish_5dpf_9dpf_adult_integrated_mg.* datasets can be accessed at:

Celotto L, Rost F, Machate A, Bläsche J, Dahl A, Weber A, Hans S, Brand M; 2023; Single cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration; NCBI GEO; GSE226373

Krylov A, Yu S, Newton A, He J, Jusuf PR; 2023; Quiescent Müller glia heterogeneity influences regenerative response following photoreceptor ablation in the zebrafish retina; NCBI GEO; GSE218107

Yamagata, M., Yan, W., & Sanes, J. R.; 2021; A cell atlas of the chick retina based on single-cell transcriptomics; Broad Institute Single Cell Portal; [https://singlecell.broadinstitute.org/single_cell/study/SCP1159](https://singlecell.broadinstitute.org/single_cell/study/SCP1159)

Li, J., Choi, J., Cheng, X., Ma, J., Pema, S., Sanes, J. R., ... & Chen, R.; 2024; MRCA: scRNA-seq of the mouse retina - all cells; CZ CELLXGENE Discover; [https://datasets.cellxgene.cziscience.com/7dd3c81c-3f6b-4dfe-bc4c-f1f0c4dd9e3d.h5ad](https://datasets.cellxgene.cziscience.com/7dd3c81c-3f6b-4dfe-bc4c-f1f0c4dd9e3d.h5ad)

Kriukov, E., Soucy, J. R., Labrecque, E., & Baranov, P.; 2025; Human Fetal Retina Atlas; CZ CELLXGENE Discover; [https://datasets.cellxgene.cziscience.com/860a9839-5d24-4073-9a67-6ad570f41da1.h5ad](https://datasets.cellxgene.cziscience.com/860a9839-5d24-4073-9a67-6ad570f41da1.h5ad)

Li, J., Wang, J., Ibarra, I. L., Cheng, X., Luecken, M. D., Lu, J., ... & Chen, R.; 2026; Dataset scRNA-seq of human retina - all cells; CZ CELLXGENE Discover; [https://datasets.cellxgene.cziscience.com/ab675437-97bc-499c-a4ee-977a6bd414ec.h5ad](https://datasets.cellxgene.cziscience.com/ab675437-97bc-499c-a4ee-977a6bd414ec.h5ad)

 

The raw SRA data used for the de novo data generated in this study can be accessed at NCBI GEO:

Storey, S. S., Hehr, C. L., Standing, S., McFarlane, S.; 2026; Single cell atlas of the 5dpf Zebrafish retina; NCBI GEO; GSE319514.