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Single-cell RNA-seq provides insight into the underdeveloped immune system of germ-free mice

ABSTRACT: Single-cell RNA-seq provides insight into the underdeveloped immune system of germ-free mice

PROVIDER: PRJNA1253696 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33239247_1.fastq.gz	Fastqsanger.gz
	SRR33239247_2.fastq.gz	Fastqsanger.gz
	SRR33239248_1.fastq.gz	Fastqsanger.gz
	SRR33239248_2.fastq.gz	Fastqsanger.gz
	SRR33239249_1.fastq.gz	Fastqsanger.gz

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Single-cell RNA-seq provides insight into the underdeveloped immune system of germ-free mice

Project description:Germ-free mice feature a profoundly underdeveloped immune system. Despite recent studies that emphasize the role of specific bacteria-derived metabolites in immune cell development and differentiation, it remains unclear how the lack of microbiota leads to immune deficiencies. Here, we performed droplet-based single-cell RNA sequencing to analyze the bone marrow and peripheral blood of both germ-free and specific pathogen-free mice, identifying 25 distinct cell types. Our findings suggest that neutrophil apoptosis in germ-free mice may be associated with the absence of niacin dehydrogenase, which is derived primarily from Pseudomonas. In addition, germ-free mice exhibited elevated excretion of 5’-methylthioadenosine, increased ERK activation induced by reactive oxygen species, and cessation of the bone marrow stromal antigen 2 signaling pathway in germ-free mice. The responses of monocytes and CD8+ T cells to interferon β and interferon γ were reduced in germ-free mice, which explains their increased susceptibility to viruses. Together, we identified a regulatory mechanism that connects immunodeficiency with the absence of microbiota in germ-free mice and validated these findings using multiple techniques.

2025-04-25 | GSE295200 | GEO

Transcriptome of pig whole blood microRNAs provides insight into immune system development

Project description:Transcriptome of pig whole blood microRNAs provides insight into immune system development

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GNPS 3D Germ Free and Specific Pathogen Free Mice

Project description:A collection of metabolomes from organs of germ free and specific pathogen free mice.

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Germ-free and anti-biotic treated rats

Project description:The objective of the study was identify hepatic genes with expression by deprivation of gut flora. Two models were used: model 1 (study 1443KR) examined germ-free Sprague Dawley and model 2 (1512KR) examined antibiotic treated Han Wistar rats. Germ-free vs. non-germ-free, antibiotic treated vs. untreated

2010-08-31 | E-GEOD-21937 | biostudies-arrayexpress

Variability of gene expression profiles in neutrophils from Germ-free mice

Project description:Neutrophils, key cells of the innate immune system, are responsible for preventing bacterial infections. It was already demonstrated that albeit neutrophils synthesize lower levels of protein and RNA they are able to marked change its gene expression after bacteria exposure. The absence of microbial stimulation has consequences on development of the mucosal immune system as demonstrated using germ-free mice as a model. We are interested in understanding if commensal flora induces changes in the gene expression profile of neutrophils in its site of production, the bone marrow. Total RNA obtained from isolated neutrophils from Bone Marrow from Germ-free mice and control

2013-03-30 | E-GEOD-43511 | biostudies-arrayexpress

Amydala transcriptome changes in germ-free mice

Project description:We sequenced mRNA from 12 samples extracted from mouse amygdala tissue to generate the first amygdala-specific murine transcriptome for germ-free mice (GF), conventionally raised controls (CON) and germ-free mice that have been colonized with normal microbiota from postnatal day 21 (exGF).

2015-07-09 | GSE66828 | GEO

Local ancestry inference provides insight into Tilapia breeding programmes

Project description:Local ancestry inference provides insight into Tilapia breeding programmes

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Tissue neutrophil heterogeneity in germ free mice

Project description:Purpose: The goals of this study are to compare bulk RNAseq profiles of tissue neutrophils in germ free mice. Methods: Bulk RNAseq of sorted neutrophils from spleen, blood, lung from spf and germ free mice, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with RSEM.

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Aortic microRNA expression in germ-free mice and pathogen-free mice

Project description:To understand the effect of microbes on microRNAs in aorta, in this study, we examined expression of microRNA in the aorta of male (10 weeks old) germ-free mice and pathogen-free mice (control).

2016-09-15 | GSE64630 | GEO

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

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