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

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

PROVIDER: PRJNA995776 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25308642.fastq.gz	Fastqsanger.gz
	SRR25308643.fastq.gz	Fastqsanger.gz
	SRR25308644.fastq.gz	Fastqsanger.gz
	SRR25308645.fastq.gz	Fastqsanger.gz
	SRR25308646.fastq.gz	Fastqsanger.gz

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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

2023-12-22 | GSE237588 | GEO

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

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.

2023-09-01 | GSE237328 | GEO

Expression profiling of purified cells after (mature) paneth cell depletion.

Project description:We used transgenic mice expressing diphtheria toxin in a paneth cell specific manner to eablate paneth cells, but found that we could still detect and also purify (paneth) cells in the transgenic mice. We purified this population and a control WT population of paneth cells for expression profiling, with the goal to check if the diphtheria toxin expression system had low penetrance or if our PC population in TG mice was immature , and thus did not yet express the active diphtheria toxin.

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Subtherapeutic antibiotics alter the murine colonic microbiome and early life adiposity

Project description:Early life exposure to antibiotics alters the gut microbiome. These alterations lead to changes in metabolic homeostasis and an increase in host adiposity. We used microarrays to identify metabolic genes that may be up- or down-regulated secondary to antibiotic exposure. Low dose antibiotics have been widely used as growth promoters in the agricultural industry since the 1950’s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we hypothesized that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities. We generated a model of adiposity by giving subtherapeutic antibiotic therapy (STAT) to young mice and evaluated changes in the composition and capabilities of the gut microbiome. STAT administration increased adiposity in young mice and altered hormones related to metabolism. We observed substantial taxonomic changes in the microbiome, changes in copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids (SCFA), increases in colonic SCFA levels, and alterations in the regulation of hepatic metabolism of lipids and cholesterol. In this model, we demonstrate the alteration of early life murine metabolic homeostasis through antibiotic manipulation. C57BL6 mice were divided into low-dose penicillin or control groups. Given antibiotics via drinking water after weaning. Sacrificed and liver sections collected for RNA extraction.

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RNA-seq of crypt and villus cells from small intestinal epithelium from mice treated with antibiotics with an intestinal-epithelial specific deletion of LSD1 compared to wild type

Project description:To assess the role of LSD1 in mouse small intestinal epithelium, we isolated small intestinal crypts and villus from wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (cKO) (Villin-Cre+; Lsd1f/f) mice. This experiment uses a new Cre strain with 100% recombination efficiency. RNA was directly isolated from the crypt and villus, and this was used for RNAseq. Gene expression analysis of cKO derived crypt and villus provides a spatially restricted outlook on the maturation status of the intestinal epithelium in the villi and the absence of Paneth cells in the crypt. Additionally, these mice were treated with antibiotics to study epithelium intrinsic changes related to LSD1 deletion but independent of the bacterial microbiome.

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Project description:Expression profiling of purified cells after (mature) paneth cell depletion.

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

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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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