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Littermate vs co-housing mice

ABSTRACT: Comparison of co-housing and littermate methods for microbiota standardization in mouse models

PROVIDER: PRJEB28381 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2784320_1.fastq.gz	Fastqsanger.gz
	ERR2784320_2.fastq.gz	Fastqsanger.gz
	ERR2784330_1.fastq.gz	Fastqsanger.gz
	ERR2784330_2.fastq.gz	Fastqsanger.gz
	ERR2784340_1.fastq.gz	Fastqsanger.gz

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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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Project description:Purpose: To identify the impact of thermoneutral housing as opposed to standard housing on gene expression profiles in the mouse peripheral blood mononuclear cells (PBMCs), focusing on proinflammatory immune responses and high-fat diet induced non-alcoholic fatty liver disease pathogenesis. Methods: Expression profiles from PBMCs collected from C57Bl6 mice fed chow or high-fat diet for 8 weeks, following 2 weeks at either standard or thermoneutral housing conditions. Sequencing was performed in duplicate, the Illumina HiSeq 2500. Transcripts that passed quality filters were analyzed at the gene level, using Strand NGS for accurate alignment and quantification. Results: We mapped approximately 20million reads per sample to the mm10 genome using annotations produced by Ensembl, which represented 36186 transcripts. Approximately 14000 genes exhibited reasonable expression in at least one experimental condition. The primary focus was the effect of housing temperature while holding diet consistent (i.e. thermoneutral vs standard, both on high-rat diet), where ~2700 genes exhibited differential regulation. Conclusions: We present the transcriptomic profile of PBMCs from mice fed chow of high-fat diets, following either standard or thermoneutral housing. We obseve an augmented proinflammatory immune response.

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