Single Cell RNA Sequencing of adult WT Zebrafish Retina
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ABSTRACT:
PROVIDER: PRJNA982720 | ENA |
REPOSITORIES: ENA
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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:Purpose: Investigate the molecular determinants of retinal regeneration in adult vertebrates by analyzing the gene expression profiles of control and post-lesion retina of adult zebrafish, a system that regenerates following injury. Methods: Gene expression profiles of zebrafish retina and brain were determined with DNA microarray, RT-PCR, and real-time quantitative PCR analyses. Damaged retinas and their corresponding controls were analyzed 2-5 days post-lesion (acute injury condition) or 14 d post-lesion (cell regeneration condition). Results: Expected similarities and differences in the gene expression profile of zebrafish retina and brain were observed, confirming the applicability of the gene expression techniques. Mechanical lesion of retina triggered significant, time-dependent changes in retinal gene expression. The induced transcriptional changes were consistent with cellular phenomena known to occur, in a time-dependent manner, subsequent to retinal lesion, including cell cycle progression, axonal regeneration, and regenerative cytogenesis. Conclusions: The results indicate that retinal regeneration in adult zebrafish involves a complex set of induced, targeted changes in gene transcription, and suggest that these molecular changes underlie the ability of the adult vertebrate retina to regenerate. Keywords: time course; injury response; cellular correlation Control brain and retina (unlesioned); Control and lesioned retina (matched animals, at least n = 8 for each condition).
2005-09-16 | E-GEOD-3303 | biostudies-arrayexpress
Project description:Purpose: Investigate the molecular determinants of retinal regeneration in adult vertebrates by analyzing the gene expression profiles of control and post-lesion retina of adult zebrafish, a system that regenerates following injury. Methods: Gene expression profiles of zebrafish retina and brain were determined with DNA microarray, RT-PCR, and real-time quantitative PCR analyses. Damaged retinas and their corresponding controls were analyzed 2-5 days post-lesion (acute injury condition) or 14 d post-lesion (cell regeneration condition). Results: Expected similarities and differences in the gene expression profile of zebrafish retina and brain were observed, confirming the applicability of the gene expression techniques. Mechanical lesion of retina triggered significant, time-dependent changes in retinal gene expression. The induced transcriptional changes were consistent with cellular phenomena known to occur, in a time-dependent manner, subsequent to retinal lesion, including cell cycle progression, axonal regeneration, and regenerative cytogenesis. Conclusions: The results indicate that retinal regeneration in adult zebrafish involves a complex set of induced, targeted changes in gene transcription, and suggest that these molecular changes underlie the ability of the adult vertebrate retina to regenerate. Keywords: time course; injury response; cellular correlation
2005-09-16 | GSE3303 | GEO
Project description:To investigate the role of srrm3 as a regulator of retina microexons (RetMICs) we have sequenced adult retina from WT animals, and enucleated eyes from 5 dpf larvae WT and KO for srrm3.
2022-07-01 | GSE180778 | GEO
Project description:Single cell RNA-seq of adult human neural retina
| PRJEB29298 | ENA
Project description:Vertebrate vision is mediated by two kinds of photoreceptors, rods and cones, responsible for dim- and bright-light vision, respectively. Gene expression differences among cone subtypes remain poorly understood compared with rods. We generated single-cell transcriptome data using a droplet-based approach to reveal the extent of gene expression diversity among adult zebrafish photoreceptor subtypes. Populations of photoreceptor cells were enriched by using the transgenic zebrafish lines, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg, which express GFP in rods and all cone subtypes, respectively. By analyzing the single-cell transcriptomes, we found that in addition to the four canonical zebrafish cone types (ultraviolet, blue, green and red), there exist subpopulations of green and red cones in the ventral retina that express red-shifted opsin paralogs (opn1mw4 and opn1lw1). This work lays a foundation for future studies aimed at understanding how molecular differences among cone subtypes affect photoreceptor function.
2021-08-30 | GSE175929 | GEO
Project description:Thyroid hormone (TH) signaling plays an important role in the regulation of long-wavelength vision in vertebrates. In the retina, thyroid hormone receptor β (thrb) is required for expression of long-wavelength-sensitive opsin (lws) in red cone photoreceptors; whereas in retinal pigment epithelium (RPE), TH regulates expression of a cytochrome P450 enzyme, Cyp27c1, that converts vitamin A1 into vitamin A2 to produce a red-shifted chromophore. To better understand how TH controls these processes, we analyzed the phenotype of zebrafish with mutations in the three known TH nuclear receptor transcription factors (thraa, thrab, and thrb). We found that no single TH nuclear receptor is required for TH-mediated induction of cyp27c1 but that deletion of all three (thraa-/-;thrab-/-;thrb-/-) completely abrogates its induction and the resulting conversion of A1- to A2-based retinaldehydes. In the retina, loss of thrb resulted in an absence of red cones at both larval and adult stages without disruption of the underlying cone mosaic. RNA-seq analysis revealed significant downregulation of only five genes in adult thrb-/- retina, of which three (lws1, lws2, and miR-726) occur in a single syntenic cluster. In the larval thrb-/- retina, retinal progenitors destined to become red cones were transfated to ultraviolet (UV) cone opsin (sws1)-expressing cells and cells resembling horizontal cells. Taken together, our findings demonstrate cooperative regulation of cyp27c1 by TH receptors and a requirement for thrb in red cone fate determination. Thus, TH signaling coordinately regulates both spectral sensitivity and sensory plasticity.
2020-05-06 | GSE143312 | GEO
Project description:Zebrafish Retina thrb-/- RNA-seq
| PRJNA599983 | ENA
Project description:Single-cell RNA-seq and ATAC-seq of zebrafish retina
| PRJNA633835 | ENA
Project description:We found that the zebrafish non-coding element careg, which is induced in regenerating fins and heart, also participates in retina regeneration. Its activation persisted mostly in Müller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration, we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells, we performed a single-cell RNA sequencing (scRNA-seq) experiment of retinas dissected from adult careg:EGFP zebrafish at 3, 7, and 10 dpMNU. Our control retinas were dissected from fish at 3 days after treatment with heat-inactivated MNU
2023-05-10 | GSE202212 | GEO