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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

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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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.

2012-06-30 | E-GEOD-38880 | biostudies-arrayexpress

Subtherapeutic antibiotics alter the murine colonic microbiome and early life adiposity

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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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Gene expression by RNA-seq in purified paneth cells of WT and panetch cell specific P55 KO mice 3 hours after TNF

Project description:The study of how gene expression in paneth cells changes 3 hours after TNF admistration in mice were the TNFR1 (P55) genes was deleted in paneth cells using Defa6-cre.

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Project description:The most clinically relevant risk factor for Clostridioides difficile-associated disease (CDAD) is recent antibiotic treatment. Though most broad-spectrum antibiotics significantly disrupt the structure of the gut microbiota, only particular ones increase CDAD risk, suggesting additional factors might increase the risk from certain antibiotics. Here we show that commensal-independent effects of antibiotics collectively prime an in vitro germ-free human gut for CDAD. We found a marked loss of mucosal barrier and immune function with CDAD-associated antibiotic pretreatment distinct from pretreatment with an antibiotic unassociated with CDAD, which did not reduce innate immune or mucosal barrier functions. Importantly, pretreatment with CDAD-associated antibiotics sensitized mucosal barriers to C. difficile toxin activity in primary cell-derived enteroid monolayers. These data implicate commensal-independent host changes in the increased risk of CDAD with specific antibiotics. Our findings are contrary to the previously held belief that antibiotics allow for CDAD solely through disruption of the microbiome. We anticipate this work to suggest potential avenues of research for host-directed treatment and preventive therapies for CDAD, and to impact human tissue culturing protocols.

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Project description:An indepth analysis of Paneth cell transcriptome at single cell level has not been available. Existing intestinal epithelial cell scRNA dataset contain many cell types, where Paneth cells represent a small portion. We used a flow cytometry based approach to enrich and isolate relatively pure Panethc cells from a newly developed Paneth cell reporter mouse line (Lyz1-3'UTR-IRES-CreER; Rosa26R-tdTomato). Single cell RNA sequencing was performed on purified duodenal and ileal Paneth cells of mice housed under specific pathogen free condition.

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transcriptome of purified PC and non-PC fractions: GR-WT & GR-KO

Project description:Paneth Cells (PCs) are secretory cells located in the crypts of Lieberkühn of the small intestine. They produce antimicrobial peptides (AMPs) and are thought to keep the microbiome under control. The cytokine TNF, which functions mainly via its TNF receptor 1 (TNFR1 or P55), is a driving force in many inflammatory bowel disease (IBD) patients, but its impact on PCs is poorly known. We have generated intestinal glucocorticoid receptor knockout mice (GR villin KO) and investigated the diffrences between WT and KO paneth and non-paneth cell fractionf from the cell sorting.

2024-06-17 | GSE269510 | GEO

Impact of preoperative antibiotics on integrated microbiome-host transcriptomic data generated from colorectal cancer resections.

Project description:Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases. Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer (CRC) resections. We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors. To assess the impact of preoperative antibiotics on integrated microbiome and human transcriptomic data generated from archived frozen CRC resection samples. Genomic DNA (gDNA) and RNA were extracted from 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center. 16S rRNA gene sequencing (V3V4 region, paired end (PE), 300 bp) and confirmatory quantitative polymerase chain reaction (qPCR) assays were conducted on gDNA. RNA sequencing IPE, 125bp) was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers (RIN) scores ≥ 6.

2021-04-21 | GSE165255 | GEO

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