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ABSTRACT: topsoil depths

PROVIDER: PRJNA478576 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR7464230_1.fastq.gz	Fastqsanger.gz
	SRR7464230_2.fastq.gz	Fastqsanger.gz
	SRR7464240_1.fastq.gz	Fastqsanger.gz
	SRR7464240_2.fastq.gz	Fastqsanger.gz
	SRR7464231_1.fastq.gz	Fastqsanger.gz

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Project description:Exposure to less hygienic conditions during early childhood has been associated with stimulation and development of the immune system. A recent study indicated exposure of piglets to soil-borne microbes during lactation was related with modulation of gut microbiota and immune function. To identify potential molecular mechanisms and pathways impacted by early life topsoil exposure, we analyzed gene expression (mRNA and miRNA) in peripheral blood mononuclear cells (PBMC) from these piglets. Total RNA was extracted from PBMC of piglets exposed to topsoil only from d 4-d 21 of life (mRNA n=6; miRNA n=5) or unexposed control pigs (mRNA n=6; miRNA n=8) at 11, 20, and 56 days of age. Small RNA and mRNA were sequenced with 50-bp single-end reads using Illumina chemistry. Differential expression (DE) analysis was performed using PROC Glimmix of SAS to evaluate changes in expression due to topsoil exposure over time with genes declared DE at a false discovery rate (FDR) of q<0.10. A total of 138 mRNA and 21 miRNAs were identified as DE for the treatment by age interaction. Ontology enrichment analysis of DE mRNA revealed GO terms directly involved in the connection between T-cell and antigen-presenting cells that are associated with T-cell activation. Key regulatory genes identified include PTPRJ, ITGB3, TRBV30, CD3D, mir-143, mir-29, and mir-148a. While these results require validation, this study provides data supporting the hypothesis that less hygienic environments during early life may contribute to the development of the immune system

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