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

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

PROVIDER: PRJNA984608 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24949729_1.fastq.gz	Fastqsanger.gz
	SRR24949729_2.fastq.gz	Fastqsanger.gz
	SRR24949730_1.fastq.gz	Fastqsanger.gz
	SRR24949730_2.fastq.gz	Fastqsanger.gz
	SRR24949731_1.fastq.gz	Fastqsanger.gz

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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.

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A Single Cell RNA Sequence Atlas of the Early Drosophila Larval Eye

Project description:TheDrosophilaeye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis. However, a single cell RNA sequence resource that captures gene expression dynamics from the initiation of differentiation to the specification of different cell types in the larval eye disc is lacking. Here, we report transcriptomic data from 13,000 cells that cover six developmental stages of the larval eye. Our data show cell clusters that correspond to all major cell types present in the eye disc ranging from the initiation of the morphogenetic furrow to the differentiation of each photoreceptor cell type as well as early cone cells. We identify dozens of cell type-specific genes whose function in different aspects of eye development have not been reported. These single cell data will greatly aid research groups studying different aspects of early eye development and will facilitate a deeper understanding of the larval eye as a model system.

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

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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

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

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