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| Status |
Public on May 13, 2021 |
| Title |
Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [single-cell RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study were to identify expression patterns in foveal versus parafoveal cells isolated from the human retina.
Methods: Independent libraries were prepared for foveal and parafoveal cells isolated from four human donors (donors 5-8). A foveal (1 mm) and parafoveal (4 mm) punch of neural retina was acquired from each donor. Each punch of neural retina was gently dissociated in papain (Worthington biochemical) for 1.25 hours before cryopreservation. Thawed cells were barcoded with the 10X chromium and resulting libraries were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build GRCh38 with CellRanger(v3.0.1) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Libraries from single-cell donors 5-8 were aggregated using canonical correlation analysis. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1).
Results: A total of 34,493 cells were recovered after filtering with 139,962,070 corresponding reads. A total of 5,856 cells were recovered from foveal libraries while 28,637 cells were recovered from the parafoveal libraries. Clusters were assigned to known retinal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from the fovea versus the parafovea. Particular emphasis was given to regionally expressed genes in cone photoreceptor cells and Muller cells.
Conclusions: This study provides a transcriptomic comparison of the foveal and parafoveal human retina at the bulk and single-cell levels. The foveal retina is transcriptomically distinct from the directly surrounding parafovea.
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| Overall design |
mRNA profiles for thousands of cells from foveal and parafoveal retina were generated from four human donor eyes (single-cell donors 5-8) using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina NovaSeq.
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| Contributor(s) |
Scheetz TE, Voigt AP, Mullins RF |
| Citation(s) |
34014299 |
| Submission date |
Mar 16, 2021 |
| Last update date |
Aug 12, 2021 |
| Contact name |
Andrew Voigt |
| Organization name |
University of Iowa
|
| Street address |
375 Newton Road
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52246 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE169048 |
Human photoreceptor cells from different macular subregions have distinct transcriptional profiles |
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| Relations |
| BioProject |
PRJNA714963 |
| SRA |
SRP310949 |
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