HCA Data Explorer

A single-cell transcriptome atlas of the adult human retina

The retina is a specialized neural tissue that senses light and initiates image processing. Although the functional organization of specific retina cells has been well studied, the molecular profile of many cell types remains unclear in humans. To comprehensively profile the human retina, we performed single‐cell RNA sequencing on 20,009 cells from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct cell populations representing all known neural retinal cells: rod photoreceptors, cone photoreceptors, Müller glia, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, astrocytes, and microglia. Our data captured molecular profiles for healthy and putative early degenerating rod photoreceptors, and revealed the loss of MALAT1 expression with longer post‐mortem time, which potentially suggested a novel role of MALAT1 in rod photoreceptor degeneration. We have demonstrated the use of this retina transcriptome atlas to benchmark pluripotent stem cell‐derived cone photoreceptors and an adult Müller glia cell line. This work provides an important reference with unprecedented insights into the transcriptional landscape of human retinal cells, which is fundamental to understanding retinal biology and disease.

Raymond CB WongCentre for Eye Research Australiawongcb@unimelb.edu.au
Samuel W Lukowski (Computational Scientist)1
Camden Y Lo (Computational Scientist)2
Alexei A Sharov (Computational Scientist)3
Quan Nguyen (Computational Scientist)1
Lyujie Fang (Experimental Scientist)4
Sandy SC Hung (Experimental Scientist)4
Ling Zhu (Experimental Scientist)5
Ting Zhang (Experimental Scientist)5
Ulrike Grünert (Experimental Scientist)5
Tu Nguyen (Experimental Scientist)4
Anne Senabouth (Experimental Scientist)1
Jafar S Jabbari (Experimental Scientist)6
Emily Welby (Experimental Scientist)7
Jane C Sowden (Principal Investigator)7
Hayley S Nguyen (Biomaterial Provider)4
Adrienne Mackey (Biomaterial Provider)4
Graeme Pollock (Biomaterial Provider)4
Trevor D Lamb (Principal Investigator)8
Peng-Yuna Wang (Principal Investigator)9
Alex W Hewitt (Principal Investigator)4
Mark C Gillies (Principal Investigator)5
Joseph E Powell (Principal Investigator)10
Raymond CB Wong (Principal Investigator)4
1University of Queensland
2Monash University
3National Institutes of Health
4Centre for Eye Research Australia
5University of Sydney
6Australian Genome Research Facility
7UCL Great Ormond Street Institute of Child Health
8The Australian National University
9Swinburne University of Technology
10Garvan Institute of Medical Research
Marion F Shadbolt

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Analysis Portals


Project Label



Homo sapiens

Sample Type


Anatomical Entity


Organ Part

retinal neural layer

Selected Cell Types


Disease Status (Specimen)


Disease Status (Donor)

2 disease statuses

Development Stage

human adult stage

Library Construction Method

10x 3' v2

Nucleic Acid Source

single cell

Paired End


File Format

5 file formats

Cell Count Estimate


Donor Count

bam5 file(s)csv1 file(s)fastq.gz15 file(s)loom6 file(s)zip7 file(s)