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| Status |
Public on Jun 22, 2020 |
| Title |
Cell atlas of the human fovea and peripheral retina |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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 reti-na of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal gangli-on and non-neuronal cells. Nearly all types are shared between the two retinal re-gions, 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 dis-eases. Many are expressed in striking cell class-, type-, or region-specific patterns. Fi-nally, 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 pro-vide a foundation for investigating molecular mechanisms underlying visual pro-cessing.
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| Overall design |
To generate a comprehensive cell atlas of human retina, we obtained eight retinas from seven genetically unrelated human donors with no clinical history of ocular disease. We dissected fovea (~1.5 mm diameter centered on the foveal pit, which was visible under a dissecting microscope) and peripheral samples (> 5 mm from the fovea) from whole retina, pooling peripheral pieces from all four quadrants. Foveal samples were dissociated into single cells, which were profiled without further processing using high-throughput droplet sequencing. For peripheral samples, in which rod photoreceptors and RGC comprise ~80% and <2 % of total cells respectively, we depleted rods using magnetic beads conjugated to anti-CD73 or enriched RGCs using anti-CD90-conjugated beads prior to collection , using protocols established in our study on macaque retina. Libraries were prepared from foveal and peripheral samples, and sequenced. Altogether, we obtained 84,982 high-quality transcriptomes, 55,736 from fovea and 29,246 from peripheral retina. The median number of unique transcripts captured per cell was 2,577 and the median number of genes detected was 1,308.
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| Contributor(s) |
Yan W, Peng Y, van Zyl T, Regev A, Shekhar K, Juric D, Sanes JR |
| Citation(s) |
32555229 |
| Submission date |
Apr 03, 2020 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Wenjun Yan |
| E-mail(s) |
wey334@g.harvard.edu
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| Organization name |
Harvard University
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| Department |
Department of Molecular and Cellular Biology
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| Lab |
Joshua Sanes
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| Street address |
52 Oxford Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA623011 |
| SRA |
SRP255195 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148077_count_mat_donor_H1.csv.gz |
24.8 Mb |
(ftp)(http) |
CSV |
| GSE148077_count_mat_donor_H11.csv.gz |
9.2 Mb |
(ftp)(http) |
CSV |
| GSE148077_count_mat_donor_H2.csv.gz |
12.2 Mb |
(ftp)(http) |
CSV |
| GSE148077_count_mat_donor_H3.csv.gz |
44.4 Mb |
(ftp)(http) |
CSV |
| GSE148077_count_mat_donor_H4.csv.gz |
9.0 Mb |
(ftp)(http) |
CSV |
| GSE148077_count_mat_donor_H5.csv.gz |
65.1 Mb |
(ftp)(http) |
CSV |
| GSE148077_count_mat_donor_H9.csv.gz |
9.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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