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Single-cell gene expression profie of developing photoreceptor cells in larval zebrafish

ABSTRACT: Single-cell gene expression profie of developing photoreceptor cells in larval zebrafish

PROVIDER: PRJNA1053781 | ENA |

REPOSITORIES: ENA

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Single-cell gene expression profie of developing photoreceptor cells in larval zebrafish

Project description:Molecular underpinnings of vertebrate retinal differentiation and maturation are poorly understood, particularly for non-mammalian species. We generated single-cell transcriptome data from the larval zebrafish retina and characterized gene expression diversity among photoreceptor subtypes and their progenitors.

2024-10-23 | GSE250379 | GEO

Single-cell profiling of photoreceptor cells in adult zebrafish

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

Single-cell profiling of photoreceptor cells in adult zebrafish

Project description:Single-cell profiling of photoreceptor cells in adult zebrafish

| PRJNA734313 | ENA

A Single Cell Genomics Atlas of the Drosophila Larval Eye Reveals Distinct Developmental Timelines and Novel Markers for All Photoreceptor Subtypes

Project description:The Drosophila eye is a powerful model system to study the dynamics of cell differentiation, cell state transitions, cell maturation, and pattern formation. However, a high-resolution single cell genomics resource that accurately profiles all major cell types of the larval eye disc and their spatiotemporal relationships is lacking. Here, we report transcriptomic and chromatin accessibility data for all known cell types in the developing eye. Photoreceptors appear as strands of cells that represent dynamic developmental timelines. Photoreceptor subtypes are transcriptionally distinct when they begin to differentiate, but then appear to assume a common transcriptome as they mature. We identify novel cell type maturation genes, enhancers, and potential regulators, as well as genes with distinct R3 or R4 photoreceptor specific expression. Finally, we observe that photoreceptor chromatin accessibility is more permissive than non-neuronal lens-secreting cone cells, which show a more restrictive chromatin profile. These single cell genomics atlases will greatly enhance the power of the Drosophila eye as a model system.

2023-08-30 | GSE235110 | GEO

Retinoic acid signaling targets within the embryonic zebrafish eye during photoreceptor differentiation

Project description:The signaling molecule retinoic acid (RA) regulates rod and cone photoreceptor fate, differentiation, and survival. The purpose of this study was to identify eye-specific genes controlled by RA during photoreceptor differentiation in the zebrafish. 6 samples; 3 replicates of 2 conditions

2015-08-28 | E-GEOD-63873 | biostudies-arrayexpress

Transcriptome profiling of developing photoreceptor subtypes reveals candidate genes for avian photoreceptor diversification

Project description:Purpose: Avian photoreceptors are a diverse class of neurons, comprised of four single cones, the two members of the double cone, and rods. Many distinctive features of photoreceptor subtypes, including spectral tuning, oil droplet size and pigmentation, synaptic targets and spatial patterning, have been well characterized, but the molecular mechanisms underlying these attributes have not been explored. Furthermore, the signaling events and transcriptional regulators driving the differentiation of these diverse photoreceptors are currently unknown. Methods: To identify genes specifically expressed in distinct chicken (Gallus gallus) photoreceptor subtypes, we developed fluorescent reporters that label photoreceptor subpopulations, isolated these subpopulations using fluorescence-activated cell sorting, subjected them to next-generation sequencing, and conducted differential expression analysis. Results: We identified hundreds of differentially expressed genes from photoreceptor subpopulations labeled with rhodopsin, red opsin, green opsin, and violet opsin reporters. These genes are involved in a variety of processes, including phototransduction, transcriptional regulation, cell adhesion, maintenance of intra- and extra-cellular structure, and metabolism. Of particular note are a variety of differentially expressed transcription factors, which may drive and maintain photoreceptor diversity, and cell adhesion molecules that may mediate spatial patterning of photoreceptors and act to establish retinal circuitry. Conclusions: These analyses provide a framework for future studies that will dissect the role of these various factors in the differentiation of avian photoreceptor subtypes. mRNA expression profiling of 5 pairs of photoreceptor subtypes isolated from chicken retinal explants, 3 replicates per sample

2014-09-01 | E-GEOD-59850 | biostudies-arrayexpress

Retinoic acid signaling targets within the embryonic zebrafish eye during photoreceptor differentiation

2015-08-28 | GSE63873 | GEO

Characterization of T cells from the larval zebrafish tail via single-cell RNAseq

Project description:We report single-cell RNA sequencing of cells from the Tg(lck:GFP) larval zebrafish tail, to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells, in addition to canonical T and ubiquitous immune cell markers.

2020-05-13 | GSE137770 | GEO

A single cell transcriptome atlas of the developing zebrafish hindbrain

Project description:A single cell transcriptome atlas of the developing zebrafish hindbrain

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An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution

Project description:Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme subtypes, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.

2021-02-16 | GSE152906 | GEO

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