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The Drosophila Embryo at Single-Cell Transcriptome Resolution

ABSTRACT: The Drosophila Embryo at Single-Cell Transcriptome Resolution

OTHER RELATED OMICS DATASETS IN: GSE95025

PROVIDER: PRJNA375756 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5269550_1.fastq.gz	Fastqsanger.gz
	SRR5269550_2.fastq.gz	Fastqsanger.gz
	SRR5269560_1.fastq.gz	Fastqsanger.gz
	SRR5269560_2.fastq.gz	Fastqsanger.gz
	SRR5269551_1.fastq.gz	Fastqsanger.gz

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The Drosophila Embryo at Single-Cell Transcriptome Resolution

Project description:By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produce a virtual embryo with about 8000 expressed genes per cell. Our interactive “Drosophila-Virtual-Expression-eXplorer” (DVEX) database generates three-dimensional virtual in situ hybridizations and computes gene expression gradients. We used DVEX to uncover patterned expression of transcription factors and long noncoding RNAs, as well as signaling pathway components. Spatial regulation of Hippo signaling during early embryogenesis suggests a mechanism for establishing asynchronous cell proliferation. Our approach is suitable to generate transcriptomic blueprints for other complex tissues.

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Project description:To gain insight into the transcription programs activated during the formation of Drosophila larval structures, we carried out single cell RNA sequencing during two periods of Drosophila embryogenesis: stages 10-12, when most organs are first specified and initiate morphological and physiological specialization; and stages 13-16, when organs achieve their final mature architectures and begin to function. Our data confirm previous findings with regards to functional specialization of some organs - the salivary gland and trachea - and clarify the embryonic functions of another - the plasmatocytes. We also identify two early developmental trajectories in germ cells and uncover a potential role for proteolysis during germline stem cell specialization. We identify the likely cell type of origin for key components of the Drosophila matrisome and several commonly used Drosophila embryonic cell culture lines. Finally, we compare our findings with other recent related studies and with other modalities for identifying tissue-specific gene expression patterns. These data provide a useful community resource for identifying many new players in tissue-specific morphogenesis and functional specialization of developing organs.

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