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A single cell transcriptome atlas of the developing zebrafish hindbrain

ABSTRACT: A single cell transcriptome atlas of the developing zebrafish hindbrain

PROVIDER: PRJNA593433 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10586524.fastq.gz	Fastqsanger.gz
	SRR10586525.fastq.gz	Fastqsanger.gz
	SRR10586526.fastq.gz	Fastqsanger.gz
	SRR10586527_1.fastq.gz	Fastqsanger.gz
	SRR10586527_2.fastq.gz	Fastqsanger.gz

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Project description:Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf, 24hpf and 44hpf zebrafish hindbrains were used for single-cell RNA-sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity, dorso-ventral patterning, boundary and centre progenitor cells and temporal regulation of neurogenesis.

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Project description:Segmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at boundaries and segment centres, in part mediated by Fgf20 signalling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.

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Project description:identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish

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A single cell transcriptome atlas of the developing zebrafish hindbrain

Project description:This SuperSeries is composed of the SubSeries listed below.

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