Cell Atlas of The Human Fovea and Peripheral Retina

Wenjun Yan, Yi-Rong Peng, Tavé van Zyl, Aviv Regev, Karthik Shekhar, Dejan Juric, Joshua R. Sanes

Abstract

Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral retina of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and non-neuronal cells. Nearly all types are shared between the two retinal regions, but there are notable differences in gene expression and proportions between foveal and peripheral cohorts of shared types. We then used the human retinal atlas to map expression of 636 genes implicated as causes of or risk factors for blinding diseases. Many are expressed in striking cell class-, type-, or region-specific patterns. Finally, we compared gene expression signatures of cell types between human and the cynomolgus macaque monkey, Macaca fascicularis. We show that over 90% of human types correspond transcriptomically to those previously identified in macaque, and that expression of disease-related genes is largely conserved between the two species. These results validate the use of the macaque for modeling blinding disease, and provide a foundation for investigating molecular mechanisms underlying visual processing.

Datasets

1. Bipolar cells of the human fovea and peripheral retina
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_depletion_factors
suspension_enriched_cell_types
suspension_enrichment_factors
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
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H58959 cells
H37573 cells
H12860 cells
sanes_Pt22077 cells
H111729 cells
H91503 cells
H41207 cells
Preview
Cell Atlas of The Human Fovea and Peripheral Retina
2. Non-neuronal cells of the human fovea and peripheral retina
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_depletion_factors
suspension_enriched_cell_types
suspension_enrichment_factors
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
H36268 cells
H56009 cells
H14615 cells
sanes_Pt22219 cells
H41479 cells
H91118 cells
H11417 cells
Preview
Cell Atlas of The Human Fovea and Peripheral Retina
3. Amacrine cells of the human fovea and peripheral retina
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_depletion_factors
suspension_enriched_cell_types
suspension_enrichment_factors
suspension_uuid
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library_uuid
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mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
H37059 cells
H13855 cells
H51683 cells
H4518 cells
H11254 cells
H9139 cells
sanes_Pt299 cells
Preview
Cell Atlas of The Human Fovea and Peripheral Retina
4. Retinal ganglion cells of the human fovea and peripheral retina
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_depletion_factors
suspension_enriched_cell_types
suspension_enrichment_factors
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
H57102 cells
sanes_Pt21474 cells
H31313 cells
H1577 cells
H4514 cells
H11241 cells
H9183 cells
Preview
Cell Atlas of The Human Fovea and Peripheral Retina
5. Photoreceptor cells of the human fovea and peripheral retina
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_depletion_factors
suspension_enriched_cell_types
suspension_enrichment_factors
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
H54105 cells
H112126 cells
H92073 cells
H4395 cells
H3225 cells
sanes_Pt2112 cells
H134 cells
Preview
Cell Atlas of The Human Fovea and Peripheral Retina
6. Horizontal cells of the human fovea and peripheral retina
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_depletion_factors
suspension_enriched_cell_types
suspension_enrichment_factors
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
H31242 cells
H5871 cells
sanes_Pt2280 cells
H4227 cells
H1114 cells
H972 cells
H1162 cells
Preview
Cell Atlas of The Human Fovea and Peripheral Retina

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Source data

https://cellxgene.cziscience.com/collections/1d1c7275-476a-49e2-9022-ad1b1c793594

Alias names

GSE148077, SCP839, PMID32555229, PMC7299956

Cite this study

Yan, W., Peng, Y.R., van Zyl, T., Regev, A., Shekhar, K., Juric, D. and Sanes, J.R., 2020. Cell atlas of the human fovea and peripheral retina. Scientific reports, 10(1), p.9802. https://doi.org/10.1038/s41598-020-66092-9