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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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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.

2022-01-01 | GSE182725 | GEO

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

Project description:Gut microbiota and the circadian clock both regulate metabolism. The circadian clock and associated feeding rhythms were shown to impact on the microbial community. However, to what extent gut microbiota reciprocally affect daily rhythms of gene expression and physiology in the host remains elusive. Here, we analyzed the transcriptomes of male and female germ-free mice. While this revealed subtle changes in circadian clock gene expression in liver, intestine, and white adipose tissue, germ-free mice showed considerably altered expression of genes associated to rhythmic physiology. Strikingly, absence of microbiome severely compromised liver sex-dimorphism at the transcriptome and metabolome level. Their sex-specific rhythmicity was strongly attenuated. The resulting feminization of male and masculinization of female hepatic gene expression in germ-free animals is likely caused by altered sex-dimorphism in sex and growth hormone secretion, linked to differential activation of xenobiotic receptors. This defines a novel mechanism by which the gut microbiome regulates host metabolism.

2018-09-01 | GSE114400 | GEO

Temporal profile of germ-free and conventionally raised male mice (DUODENUM and ILEUM)

2018-09-01 | GSE114399 | GEO

Transcriptional profiling of 53 tissue samples from germ-free and conventionally raised mice

2014-01-31 | GSE31115 | GEO

Transcriptional profiling of 77 tissue samples from germ-free and conventionally raised mice.

2011-12-08 | GSE17438 | GEO

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

2018-09-01 | GSE114401 | GEO

Transcriptional profiling of 53 tissue samples from germ-free and conventionally raised mice

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.

2014-01-31 | E-GEOD-31115 | biostudies-arrayexpress

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.

2022-07-22 | E-MTAB-11984 | biostudies-arrayexpress

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

Project description: Not available

| S-EPMC4961299 | biostudies-literature

The transcriptome profiling analysis of intestines and kidneys in conventionally raised (CV) and germ-free (GF) wild type zebrafish embryos

Project description:To investigate how the zebrafish embryos respond to the absence of the microbiota, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32,948 cDNAs of the zebrafish genome assembly were annotated after reads mapping for further analysis. For the 5 dpf intestinal tissue samples, 948 genes (4% of the total number of genes) were differentially expressed, 371 genes were up-regulated and 577 genes were down-regulated in the GF group . For the 7 dpf kidney tissue samples, 697 genes (3% of the total number of genes) were differentially expressed, 341 genes were up-regulated and 356 genes were down-regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos (both in intestines at 5 dpf and in kidneys at 7 dpf). To investigate how the transcriptome changes in the chd8-/- zebrafish embryos, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively.

2023-03-15 | GSE200577 | GEO

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