Single cell RNA-seq of adult human neural retina
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ABSTRACT:
PROVIDER: PRJEB29298 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To comprehensively profile cell types in the human retina, we performed single cell RNA-sequencing on 20,009 cells obtained post-mortem from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct clusters representing all known retinal cells: rod photoreceptors, cone photoreceptors, Müller glia cells, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, retinal astrocytes and microglia.
2019-08-21 | E-MTAB-7316 | biostudies-arrayexpress
Project description:Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina. WT and GFP antibodies were used to perform two independent ChIP-seq experiments using Illumina GAIIx.
2014-01-15 | E-GEOD-54084 | biostudies-arrayexpress
Project description:Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina.
2014-01-15 | GSE54084 | GEO
Project description:Single Cell RNA Sequencing of adult WT Zebrafish Retina
| PRJNA982720 | ENA
Project description:The human neural retina is enriched for alternative splicing, and it is estimated that more than 10% of variants associated with inherited retinal diseases (IRDs) alter splicing. Previous research mainly used short-read RNA-sequencing techniques to investigate retina-specific splicing and splicing factors. However, this technique provides limited information about transcript isoforms. To gain a deeper understanding of the human neural retina and its isoforms, we generated a proteogenomic atlas that combined PacBio long-read RNA-sequencing data with mass-spectrometry and whole-genome sequencing data from three healthy human neural retina samples. RNA-sequencing revealed that one-third of all transcripts were novel, and for IRD-associated genes, even 43% were novel. The most common novel elements of these transcripts were alternative poly(A) sites, exon elongation, and intron retention. Some novel elements affect the non-coding region but for more than 50% of the novel transcripts a novel open reading frame was predicted. Using proteomics, ten novel peptides confirmed novel isoforms in five genes. Additionally, we found novel isoforms of IMPDH1, an IRD-associated gene, with supporting peptide evidence. This study provides a comprehensive overview of the transcript and protein isoforms expressed in the healthy human neural retina. Moreover, it highlights the importance of studying tissue specific transcriptomes in greater detail to better understand tissue-specific regulation and to identify disease-causing variants.
2024-10-17 | PXD045187 | Pride
Project description:In this study, we have pooled 3 adult wild-type Zebrafish retinas and performed Single-Cell RNA Sequencing. We would like to see the transcriptomic signatures of each cell type in the retina. The data provided here will provide a foundation for other studies to further investigate the transcriptomic retinal enviromnent and compare how their models differ from WT.
2023-07-03 | GSE234661 | GEO
Project description:Retinal RNA profiles from macula and periphery of each eye were generated by single-cell sequencing. M11-M14 are macula retina and P11-P14 are peripheral retina from the same 78 year old donor. M21-M24 are macula retina and P21-P24 are peripheral retina from the same 90-year-old donor.
2021-08-11 | GSE155288 | GEO
Project description: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.
2019-05-17 | GSE130636 | GEO
Project description:The developmental pathway of the neural retina (NR) and retinal pigment epithelium (RPE) has been revealed by extensive research in mice. However, the molecular mechanisms underlying the development of the human NR and RPE, as well as the interactions between these two tissues, have not been well defined. Here, we analyzed 2,421 individual cells from human fetal NR and RPE using single-cell RNA sequencing (RNA-seq) technique and revealed the tightly regulated spatiotemporal gene expression network of human retinal cells. We identified major cell classes of human fetal retina and potential crucial transcription factors for each cell class. We dissected the dynamic expression patterns of visual cycle and ligand-receptor interaction related genes in the RPE and NR. Moreover, we provided a map of disease-related genes for human fetal retinal cells and highlighted the importance of retinal progenitor cells as potential targets of inherited retinal diseases. Our findings captured the key in vivo features of the development of the human NR and RPE and offered insightful clues for further functional studies.
2019-07-04 | GSE107618 | GEO