Omics · study · 2026
Single cell atlas of the human retinal pigment epithelium and the choroid
Listed in NCBI GEO
The survival and proper function of the neural retina depend on the support of two underlying tissues: the retinal pigment epithelium (RPE) and the choroid.
Description
Dysfunction in the RPE and choroid can lead to a range of inherited and complex diseases. To better characterize the cellular, transcriptomic, and epigenomic heterogeneity and dynamics within the RPE and choroid, we conducted single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) as well as single-nucleus ATAC sequencing (snATAC-seq) on donor tissue samples.
By integrating newly generated and previously published datasets, we developed version 1 of the human RPE and choroid cell atlas. This atlas includes scRNA-seq data from 205,925 cells from 67 donors and snRNA-seq data from 742,625 nuclei from 54 donors. Additionally, we incorporated snRNA-seq data from 136,555 nuclei from developmental RPE/choroid tissues spanning post-conception weeks (PCW) 10-23.
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This comprehensive dataset enabled the identification of 15 major cell classes, which were further subdivided into 25 cell types. Additionally, open chromatin profiling was performed on over 234,007 nuclei using snATAC-seq, providing an in-depth characterization of chromatin accessibility for each cell type. As part of the Human Cell Atlas project, this resource lays a robust foundation for advancing research into the biology of the RPE and choroid and the diseases associated with these tissues.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE312nnn/GSE312791 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE312791 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1365856 ncbi.nlm.nih.gov/bioproject/PRJNA1365856 ↗
project · from NCBI GEO
- PubMed 42539169 pubmed.ncbi.nlm.nih.gov/42539169 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Genome binding/occupancy profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 65%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE312791 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[method].geo_series_type:genome-binding-occupancy-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |