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Transcriptional profiling of murine small intestine in conventional or SPF housing conditions

ABSTRACT: Transcriptional profiling of murine small intestine in conventional or SPF housing conditions

PROVIDER: PRJNA721667 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14229237.fastq.gz	Fastqsanger.gz
	SRR14229238.fastq.gz	Fastqsanger.gz
	SRR14229239.fastq.gz	Fastqsanger.gz
	SRR14229240.fastq.gz	Fastqsanger.gz
	SRR14229241.fastq.gz	Fastqsanger.gz

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Transcriptional profiling of murine small intestine in conventional or SPF housing conditions

Project description:We studied the influence of the microbiota on intestinal homeostasis and tumor development after loss of the intestinal tumor phenotype in Msh2-Lynch mice upon rederivation of the mouse line in an SPF facility. We generated RNA seq data from total RNA of small intestine (jejunum) derived from either conventional or SPF mice.

2022-02-08 | GSE171996 | GEO

Augmented murine hematopoietic stem and progenitor cell reconstruction through conventional co-housing

Project description:Background and methods: The effects of microbiota toward hematopoietic stem and progenitor cells (HSPCs) were very much complicated based on previous reports. In the current study, normal inbred C57BL6 (B6) mice from the Jackson Laboratory were maintained in the SPF environment for three weeks. Baseline complete blood counts were normal, and animals were then separated into two groups: 1) SPF mice stayed in the SPF facility, and 2) SPF mice being transferred to a conventional facility for co-housing (CVT). At one month of co-housing, we bled and euthanized animals, sorted lineage-CD117+ cells from bone marrow of SPF and CVT mice respectively, and performed single cell RNA sequencing on sorted hematopoietic stem and progenitor cells using 10XGenomics Chromium Single Cell 3' Solution and sequenced with Illumina HiSeq 3000 Systems. Results: We characterized heterogeneity of HSPCs, defined differential gene expression and performed pathway analysis. Proportion of LTHSC was lower and the proportion of GMP was higher from CVT mice than those from SPF mice. Pathway analyses of differentially-expressed genes in HSPCs we found down-regulation of genes related to immune responses and cell proliferation and activation, and up-regulation of genes associated with cellular metabolism, including protein, ribosome, and energy metabolic processes, in cells from CVT mice. Conclusion: Observations from our study demonstrated a positive effect in co-housed CVT mice that promotes HSPC reconstitution through modulation of molecular elements involving multiple signaling pathways.

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Augmented murine hematopoietic stem and progenitor cell reconstruction through conventional co-housing

Project description:Augmented murine hematopoietic stem and progenitor cell reconstruction through conventional co-housing

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Dietary antigens influence the antigen presentation pathway of small intestine epithelium

Project description:Epithelial cells of the small intestine are designed to absorb the nutrients from the diet, so we tested if the absence of dietary macromolecules and protein antigens had an impact on the physiological condition of IECs. We generated RNAseq data from small intestine IECs isolated from mice free of any conventional non-self antigens for TCRab T cells. A comparison with RNAseq data generated from IECs isolated from SPF or GF mice showed clear differences between the transcriptomes of IECs isolated from the AF, SPF or GF mice.

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Project description:The gut microbiota is closely associated with digestion, metabolism, immunity, and host health. The imbalance of the microbial community in livestock directly affects their well-being and, consequently, productivity. The composition and diversity of the gut microbiota are influenced not only by host genetics but also by environmental factors such as the microbial complexity of the rearing environment, feeds, and antibiotics. Here, we focus on the comparison of gut microbial communities in miniature pigs developed for xenotransplantation in specific pathogen-free (SPF) and conventional (non-SPF) facilities. To identify the disparities in gut microbial composition and functionality between these two environments, 16S RNA metagenome sequencing was conducted using fecal samples. The results revealed that the non-SPF pigs had higher gut microbiota diversity than the SPF pigs. The genera Streptococcus and Ruminococcus were more abundant in SPF pigs than in non-SPF pigs. Blautia, Bacteroides, and Roseburia were exclusively observed in SPF pigs, whereas Prevotella was exclusively found in non-SPF pigs. Carbohydrate and nucleotide metabolism, as well as environmental information processing, were predicted to be enriched in SPF pigs. In addition, energy and lipid metabolism, along with processes related to genetic information, cellular communication, and diseases, were predicted to be enriched in non-SPF pigs. This study makes an important contribution to elucidating the impact of environments harboring a variety of microorganisms, including pathogens, on the gut microbiota of miniature pigs. Furthermore, we sought to provide foundational data on the characteristics of the gut microbiota in genetically modified pigs, which serve as source animals for xenotransplantation.

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Project description:The effects of maternal microbiota on the fetal development was investigated by comparing tissues of fetuses from germ-free (GF) and normal (SPF) murine dams using RNA-seq and non-targeted metabolomics (for metabolomics data, see: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02457-6). For RNA-seq, two E18.5 fetuses were collected from 6 GF dams and 6 SPF dams, and transcriptomes analyzed by QuantSeq in whole intestine, brain and placenta.

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Genome-wide transcriptome profiling of Colon Intestine-Chip and Conventional Organoid Cell Culture System Using RNA-seq

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