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RNA-seq analysis of conventionally raised zebrafish larvae compared to germ-free zebrafish larvae and germ-free larvae treated with zebrafish metabolites.

ABSTRACT: RNA-seq analysis of conventionally raised zebrafish larvae compared to germ-free zebrafish larvae and germ-free larvae treated with zebrafish metabolites.

PROVIDER: PRJNA757618 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15606829_1.fastq.gz	Fastqsanger.gz
	SRR15606829_2.fastq.gz	Fastqsanger.gz
	SRR15606830_1.fastq.gz	Fastqsanger.gz
	SRR15606830_2.fastq.gz	Fastqsanger.gz
	SRR15606831_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of conventionally raised zebrafish larvae compared to germ-free zebrafish larvae and germ-free larvae treated with zebrafish metabolites.

Project description:Here, we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long-pec stage (2 days post fertilization) and sequenced at a depth of 80-100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA-Seq analysis. Of these, 42 were rescued with the treatment of zebrafish gut-derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling.

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Temporal profiles of germ-free and conventionally raised female and male mice (LIVER)

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Temporal profile of germ-free and conventionally raised male mice (epididymal white adipose tissue (WAT))

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Project description:Whole-transcriptome survey of gene expression differences between germ-free (GF) and conventionally raised (CONV-R) mice. To assess the role of toll-like receptor signalling, both wild-type and Myd88 -/- mice were used. Three different tissues were harvested from 20 mice (5 WT CONV-R, 5 Myd88 -/- CONV-R, 4 WT GF, 6 Myd88 -/- GF) and expression profiles were determines using the Affymetrix Mouse Gene 1.0ST platform.

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Single-cell RNA sequencing of germ-free zebrafish embryos

Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. We previously evaluated the impact of graphene oxide (GO) on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild-type versus AhR-deficient zebrafish. Here, we performed single-cell RNA-sequencing (10x Genomics) on whole (dissociated) germ-free (GF) zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.

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Single-cell RNA sequencing of germ-free zebrafish embryos

Project description:Single-cell RNA sequencing of germ-free zebrafish embryos

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16S rRNA amplicon sequencing dataset for conventionalized and conventionally raised zebrafish larvae.

Project description:Data presented here contains metagenomic analysis regarding the sequential conventionalization of germ-free zebrafish embryos. Zebrafish embryos that underwent a germ-free sterilization process immediately after fertilization were promptly exposed to and raised to larval stage in conventional fish water. At 6 days postfertilization (dpf), these "conventionalized" larvae were compared to zebrafish larvae that were raised in conventional fish water never undergoing the initial sterilization process. Bacterial 16S rRNA amplicon sequencing was performed on DNA isolated from homogenates of the larvae revealing distinct microbiota variations between the two groups. The dataset described here is also related to the research article entitled "Microbial modulation of behavior and stress responses in zebrafish larvae" (Davis et al., 2016) [1].

| S-EPMC4961299 | biostudies-literature

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