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| Status |
Public on Jul 11, 2022 |
| Title |
Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The anterior segment of the eye consists of the cornea, iris, ciliary body, crystalline lens and aqueous humor outflow pathways. Together, these tissues are essential for the proper functioning of the eye. Disorders of vision have been ascribed to defects in all of them; some, including glaucoma and cataract, are among the most prevalent causes of blindness. To characterize the cell types that comprise these tissues, we generated an anterior segment cell atlas of the human eye using high throughput single-nucleus RNA sequencing (snRNAseq). We profiled 191,992 single nuclei from non-diseased anterior segment tissues from 6 human donors, identifying >60 cell types. Many are discrete, whereas others in lens and cornea form continua, corresponding to known developmental transitions that persist in adulthood. Having profiled each tissue separately, we performed an integrated analysis of the entire anterior segment revealing that some cell types are unique to single structure whereas others are shared across tissues. This integrated cell atlas was then used to investigate cell type-specific expression patterns of more than >900 human ocular disease genes identified either through Mendelian inheritance patterns or genome-wide association studies (GWAS).
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| Overall design |
To build a better understanding of the complex tissues comprising the human anterior segment, we generated a cell atlas using high throughput single-nucleus RNA sequencing (snRNAseq). We profiled 191,992 single nuclei from non-diseased anterior segment tissues, applied computational methods to cluster them based on transcriptomic similarity, and used histological techniques to assign cell type identities to the clusters. After investigating each dataset independently, we pooled nuclei from multiple tissues and performed an integrated analysis. In this way, we were able to show that some cell types are confined to specific tissues whereas others are shared across two or more tissues. Finally, we used this cell atlas to investigate cell type-specific expression patterns of human ocular disease genes identified either through Mendelian inheritance patterns or genome-wide association studies (GWAS).
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| Contributor(s) |
van Zyl T, Yan W, McAdams A, Monavarfeshani A, Hageman G, Sanes JR |
| Citation(s) |
35858321 |
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| Submission date |
Mar 20, 2022 |
| Last update date |
Sep 27, 2022 |
| 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 (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (38)
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| Relations |
| BioProject |
PRJNA817894 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE199013_HumanCB_count_matrix.csv.gz |
92.1 Mb |
(ftp)(http) |
CSV |
| GSE199013_HumanCornea_count_matrix.csv.gz |
104.4 Mb |
(ftp)(http) |
CSV |
| GSE199013_HumanIris_count_matrix.csv.gz |
163.5 Mb |
(ftp)(http) |
CSV |
| GSE199013_HumanLens_count_matrix.csv.gz |
42.4 Mb |
(ftp)(http) |
CSV |
| GSE199013_HumanMacula_count_matrix.csv.gz |
118.2 Mb |
(ftp)(http) |
CSV |
| GSE199013_HumanTMCSW_count_matrix.csv.gz |
159.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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