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Series GSE236566 Query DataSets for GSE236566
Status Public on Jul 12, 2023
Title Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here we used high-throughput single nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in the extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases – for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ~151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the new data complete a “Version 1” cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
 
Overall design single nucleus RNA-seq was performed on nuclei isolated from frozen human oculartissues. Fluorescence-activated cell sorting was used to collect DAPI-positive nuclei. For each tissue, three or more biological samples were used. Approximately 8000 (for some samples less) nuclei were recovered for each sample, and each nucleuswas sequenced to a depth of~40000 reads.
 
Contributor(s) Monavarfeshani A, Yan W, Hageman GS, Sanes JR
Citation(s) 37566633
Submission date Jul 05, 2023
Last update date Oct 02, 2023
Contact name Wenjun Yan
E-mail(s) wey334@g.harvard.edu
Organization name Harvard University
Department Department of Molecular and Cellular Biology
Lab Joshua Sanes
Street address 52 Oxford Street
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (36)
GSM7553419 Donor Id: Hu0355; Eye: OS; Tissue: ON (Hu035516OSONallnuc)
GSM7553420 Donor Id: Hu0220; Eye: OS; Tissue: ON (Hu220OSON)
GSM7553423 Donor Id: Hu0221; Eye: OS; Tissue: ON (Hu221OSON)
Relations
BioProject PRJNA991576

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE236566_Count_matrix.mtx.gz 1.0 Gb (ftp)(http) MTX
GSE236566_Count_matrix_cellnames.csv.gz 692.2 Kb (ftp)(http) CSV
GSE236566_Count_matrix_genenames.csv.gz 145.1 Kb (ftp)(http) CSV
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Processed data are available on Series record
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