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Paneth cell gene expression with and wihout zinc in different microbiome contexts (antibiotics, germ-free, normal)

ABSTRACT: Paneth cell gene expression with and wihout zinc in different microbiome contexts (antibiotics, germ-free, normal)

PROVIDER: PRJNA1185219 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31316214.fastq.gz	Fastqsanger.gz
	SRR31316215.fastq.gz	Fastqsanger.gz
	SRR31316216.fastq.gz	Fastqsanger.gz
	SRR31316217.fastq.gz	Fastqsanger.gz
	SRR31316218.fastq.gz	Fastqsanger.gz

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Paneth cell gene expression with and wihout zinc in different microbiome contexts (antibiotics, germ-free, normal)

Project description:We investigated the differences in paneth cell gene expression in different intestinal microbiome contexts and with and without zinc supplementation. We used mice housed in an SPF animal house that wre untreated, mice housed in ans SPF animal house that were treated with antobiotics for 3 weeks and germ-free mice to investigated the effect of the microbiome on paneth cell gene expression. Zinc is an essential element for paneth cell fuction. Mice of each group were further divide in zinc supplemented and non-zinc supplemented drinking water subgroups. This allowed us to check if zinc would enhance the differences between SPF, atibioicts and germ-free mice or reduce them.

2025-02-26 | GSE281682 | GEO

Paneth cell gene expression profiles after zinc suplementation - exp1

Project description:Mice were given zinc as a salt (ZnSO4; 25 mM) in the drinking water for 7 days. Expression profiling with RNA-seq was performed on purified paneth cell to investigate the genome wide effects of zinc supplemenation on the paneth cell gene expression profile

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The effect of Zinc defficiency on the mouse paneth cell transcriptome in TNF context

Project description:We investigated the effect of zinc depletion on the mouse intestine, and specifically on paneth cells. Mice were placed on a zinc depleted diet for 7 weeks after which they were given TNF for 3 hours and the the effects of dietary zinc shortage on paneth cells in TNF context were investigated. A zinc is an essential element for correct paneth cell function and zinc defficiency is a human and animal health problem investigating the PC transcriptom my provide valuable insights into the exact mechanism.

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Project description:Mice were given zinc as a salt (ZnSO4; 25 mM) in the drinking water for 7 days, then mice were injected with TNF and sampling was done 3 hours after injection. Expression profiling with RNA-seq was performed on purified paneth cellq to investigate the genome wide effects of zinc supplemenation on the paneth cell gene expression profile in the conext of TNF

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Single cell RNA sequencing analysis of germ free (GF) mouse Paneth cells and microbiome-transferred exGF mouse Paneth cells.

Project description:The single cell level Paneth cell transcriptome under gnotobiotic condition has not been resolved. How gut microbiome modulates Paneth cell transcriptome at single cell level in germ-free mice was not known. We used a flow cytometry method to isolate highly pure ileal Paneth cells from germ free (GF) Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER) and from exGF Paneth cell reporter mice that were transplanted with wild type C57B/l6 mouse gut microbiota (exGF+B6M). These isolated Paneth cells were subjected to single cell RNA sequencing by 10xGenomics.

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Gene expression by RNA-seq in purified paneth cells in antibiotics microbiome depleded mice

Project description:The study of how gene expression in paneth cells changes after TNF admistration in mice were the microbiome has been depleted with broad spectrum antibiotics. The depletion of the microbiome excludes the occurence of indirect effects mediated through it by TNF on PC gene expression, only direct TNF effecs on crypt cells are measured

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Paneth cell gene expression profiles after zinc suplementation - exp1

Project description:Paneth cell gene expression profiles after zinc suplementation - exp1

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The effect of Dinc defficiency on the mouse paneth cell transcriptome

Project description:We invstigated the effect of zinc depletion on the mouse intestine, and specifically on paneth cells. Mice ere placed on a zinc depleted diet for 7 weeks after which the the effects of dietary zinc shortage on paneth cells were investigated. A zinc is an essential element for correct paneth cell function and zinc defficiency is a human and animal health problem investigating the PC transcriptom my provide valuable insights into the exact mechanism.

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Paneth cell gene expression profiles after zinc suplementation in TNF context

Project description:Paneth cell gene expression profiles after zinc suplementation in TNF context

| PRJNA1185726 | ENA

RNA-seq mouse intestines from PN, Germ-free, SPF and Antibiotics-treated mice

Project description:We hypothesized that there were genes involved in the maintenance of intestinal tolerance to commensal bacteria. These genes should meet the following criteria: expressed in intestines, upregulated in the presence of commensal bacteria and downregulated in absence of microbes. To find these genes, we collected small intestines from postnatal mice that neither affected by the bacteria nor by the food, adult mice bred in germ-free or specific pathogen-free conditions, and adult SPF mice treated with antibiotics. We therefore performed bulk RNA sequencing using these cells.

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