Year: 2019
Type: article
Abstract: ABSTRACT Gene expression profiling is an effective way to provide insights into cell function. However, for heterogeneous tissues, bulk RNA-Seq can only provide the average gene expression profile for all cells from the tissue, making the interpretation of the sequencing result challenging. Single-cell RNA-seq, on the other hand, generates transcriptomic profiles of individual cell and cell types, making it a powerful method to decode the heterogeneity in complex tissues. The retina is a heterogeneous tissue composed of multiple cell types with distinct functions. Here we report the first single-nuclei RNA-seq transcriptomic study on human neural retinal tissue to identify transcriptome profile for individual cell types. Six retina samples from three healthy donors were profiled and RNA-seq data with high quality was obtained for 4730 single nuclei. All seven major cell types were observed from the dataset and signature genes for each cell type were identified by differential gene express analysis. The gene expression of the macular and peripheral retina was compared at the cell type level, showing significant improvement from previous bulk RNA-seq studies. Furthermore, our dataset showed improved power in prioritizing genes associated with human retinal diseases compared to both mouse single-cell RNA-seq and human bulk RNA-seq results. In conclusion, we demonstrated that feasibility of obtaining single cell transcriptome from human frozen tissues to provide additional insights that is missed by either the human bulk RNA-seq or the animal models.
Source: Nature Communications
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,200
Funders: U.S. Department of Health and Human Services, Research to Prevent Blindness, Retina Research Foundation, National Institutes of Health, National Eye Institute, National Cancer Institute, Office of Research on Women's Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awards: Acquisition of the Fluidigm system to accelerate functional genomics research, G4745162879, G5241556503, G5469311512, P30 - Core Grant for Vision Research, G6044265969, G6745058807, High Throughput Genomic Sequencer at BCM Core Facility, G8522611149, G8718705427, Utah Building Interdisciplinary Research Careers in Women's Health Career Development Program, G9000264003, Molecular Basis of Human Visual System Disorders, Genetics of early onset retinal diseases, Cancer Center Support Grant, University of Utah Core Vision Research Grant
OpenAlex ID: W2995306986