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| Status |
Public on May 17, 2019 |
| Title |
Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Single-cell RNA sequencing has revolutionized cell-type specific gene expression analysis. The goals of this study are to compare cell specific gene expression patterns between retinal cell types originating from the fovea and the periphery of human eyes.
Methods: Independent libraries were prepared for foveal and peripheral samples of neural retina from three donors using the 10x Chromium system. Libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 will CellRanger(v3.0.1) and filters removed cells likely to be doublets or cells with a high proportion of mitochondrial reads. Clustering of cells with similar expression profiles was performed with Seurat (v2.3.4).
Results: Independent libraries were prepared for foveal and peripheral samples of neural retina from three donors using the 10x Chromium system. Libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 will CellRanger(v3.0.1) and filters removed cells likely to be doublets or cells with a high proportion of mitochondrial reads. Clustering of cells with similar expression profiles was performed with Seurat (v2.3.4).
Conclusions: Our study generates a large atlas of human retinal transcriptomes at the single cell level. We identified the majority of expected neural and supportive cell types, and describe regional differences in gene expression between the fovea and the periphery. Our results show that that single-cell RNA sequencing can be performed on human retina after cryopreservation, and that cone photoreceptors and Muller cells demonstrate region-specific patterns of gene expression.
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| Overall design |
mRNA profiles for thousands of cells from foveal and peripheral retinal isolates were generated from three human donor eyes using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina HiSeq 4000.
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| Contributor(s) |
Scheetz TE, Mullins RF |
| Citation(s) |
31075224 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R21 EY027038 |
Molecular Dissection of Single Foveal Cones |
THE UNIVERSITY OF IOWA |
TODD E SCHEETZ |
| P30 EY025580 |
Multidisciplinary Investigations in Visual Science |
THE UNIVERSITY OF IOWA |
Val C. Sheffield |
|
| Submission date |
May 02, 2019 |
| Last update date |
Dec 20, 2019 |
| Contact name |
Todd Scheetz |
| E-mail(s) |
todd-scheetz@uiowa.edu
|
| Organization name |
UNIVERSITY OF IOWA
|
| Street address |
3181B MERF
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA540843 |
| SRA |
SRP194595 |
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