Single cell transcriptomes from human frozen tissues can provide insight missed by either human bulk RNA-seq or animal models.

Single-cell RNA-seq is a powerful tool in decoding the heterogeneity in complex tissues by generating transcriptomic profiles of the individual cell. Baylor College of Medicine researchers report a single-nuclei RNA-seq (snRNA-seq) transcriptomic study on human retinal tissue, which is composed of multiple cell types with distinct functions. Six samples from three healthy donors are profiled and high-quality RNA-seq data is obtained for 5873 single nuclei. All major retinal cell types are observed and marker genes for each cell type are identified. The gene expression of the macular and peripheral retina is compared to each other at cell-type level. Furthermore, this dataset shows an improved power for prioritizing genes associated with human retinal diseases compared to both mouse single-cell RNA-seq and human bulk RNA-seq results.

Unsupervised clustering identifies seven major cell types in the human retina


a Clustering of 5873 human retina single-nuclei expression profiles into seven populations (right) and representation of the alignment of six datasets from three donors (left). b Profiles of known markers (PDE6A, NETO1, SLC1A3, GAD1, SEPT4, ARR3, RBPMS) in each cluster. c The proportion of the seven cell types (rod, BC, MG, AC, HC, cone, RGC) in the macular and peripheral samples (bar graph shows the mean of the proportion; single data points are visualized in dots, N = 3). d Heatmap of DEGs in each cell type and the gene ontology term enrichment by each set of DEGs. For visualization, top 50 DEGs with least FDR q-value and top five terms under the biological process category with least p-value were used. Each column represents a cell while each row represents a gene. Gene expression values are scaled across all the cells.

Liang Q, Dharmat R, Owen L, Shakoor A, Li Y, Kim S, Vitale A, Kim I, Morgan D, Liang S, Wu N, Chen K, DeAngelis MM, Chen R. (2019) Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling. Nat Commun 10(1):5743. [article]

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