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Single-cell RNA-seq of germ-free and specific pathogen-free small intestinal epithelium

ABSTRACT: Single-cell RNA-seq of germ-free and specific pathogen-free small intestinal epithelium

PROVIDER: PRJNA802047 | ENA |

REPOSITORIES: ENA

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Single-cell RNA-seq of germ-free and specific pathogen-free small intestinal epithelium

Project description:The small intestinal epithelial barrier inputs signals from the gut microbiota in order to balance physiological inflammation and tolerance, and to promote homeostasis. Understanding the dynamic relationship between microbes and intestinal epithelial cells has been a challenge given the cellular heterogeneity associated with the epithelium and the inherent difficulty of isolating and identifying individual cell types. Here, we used single-cell RNA sequencing of small intestinal epithelial cells from germ-free and specific pathogen-free mice to study microbe-epithelium crosstalk at the single cell resolution.

2022-08-15 | GSE195742 | GEO

GNPS 3D Germ Free and Specific Pathogen Free Mice

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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).

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Sorted HSCs from aged Specific Pathogen Free and germ free mice

Project description:Sorted HSCs from aged Specific Pathogen Free and germ free mice

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Global hepatic gene expression data from germ free and specific pathogen free male mice.

Project description:Liver clock regulates transcription of hepatic genes in response to feeding. To explore the possibility that the microbiome influences this process, we measured the liver transcriptome in normal mice (Specific Pathogen Free or SPF mice) and compared it to the transcriptome in mice lacking microbiota (Germ Free or GF mice) at different time points over 24h. We used microarrays to detail the global programme of gene expression in liver of GF and SPF 10-12 weeks-old male C57Bl/6 male mice. There are 40 liver samples, each from an individual mouse. The samples are from germ free mice (GF) and specific pathogen free mice (SPF). Mice of both types were sacrificed at four time points: Zeitgeber Time 0, 6, 12, and 18. There are five replicates per condition.

2016-02-20 | E-GEOD-71628 | biostudies-arrayexpress

Small RNA sequencing of lipoproteins (HDL) obtained from germ-free mice and facility matched specific-pathogen free mice.

Project description:Plasma was harvested from two cohorts of facility-matched germ free (GF) and specific-pathogen free (SPF) mice at the National Gnotobiotic Rodent Resource Center (NGRRC; North Carolina, USA). Plasma was then fractionated by size-exclusion chromatography using three tandem Superdex200 increase columns (Cytiva). Fractions corresponding with HDL were then pooled and concentrated prior to RNA isolation. Small RNA libraries were generated from total RNA using NextFlex V3 Small RNA Seq-kit (Perkin Elmer) according to manufacturer’s instructions. Equimolar amounts of each library were then pooled and sequenced on the NextSeq500 platform (Illumina). Individual libraries were then demultiplexed and analyzed with the TIGER analytical pipeline.

2022-06-29 | GSE206857 | GEO

Global hepatic gene expression data from germ free and specific pathogen free male mice.

2016-02-20 | GSE71628 | GEO

Expression analysis of colonic and small intestinal neurons in the germ-free (GF) and specifric pathogen-free (SFP) mice

Project description:Expression analysis of colonic and small intestinal neurons in the germ-free (GF) and specifric pathogen-free (SFP) mice

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Expression data from germ free (GF) and specific pathogen free (SPF) mouse wound bed

Project description:Expression data from germ free (GF) and specific pathogen free (SPF) mouse wound bed

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Expression data from germ free (GF) and specific pathogen free (SPF) mouse wound bed

Project description:Environmental factors that enhance regeneration are largely unknown. We hypothesized that skin bacteria modulate regeneration. Here, we assessed low, medium, and high levels of bacterial burden in Wound Induced Hair follicle Neogenesis (WIHN), a rare adult organogenesis model. WIHN levels and stem cell markers indeed correlated with bacterial counts, being lowest in germ free (GF), intermediate in conventional specific pathogen free (SPF), and highest even in mice infected with pathogenic Staphylococcus aureus. We identified IL-1β and keratinocyte-dependent IL-1R-MyD88 signaling as necessary and sufficient for bacteria to promote regeneration. Finally, in a small clinical trial, we found that a topical broad-spectrum antibiotic slowed skin wound healing. These results counter conventional notions that infection inhibits regeneration and the need for full sterility of small wounds.

2021-04-01 | GSE158613 | GEO

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