Data paper: Dataset describing the effects of environmental enrichment and sows’ characteristics on the peripheral blood mononuclear cell transcriptome

Abstract

Blood immune cells transcriptome can be used as a tool to investigate molecular mechanisms or identify biomarkers of several physiological processes. Factors such as reproductive status, age, or physical and mental states resulting from social and non-social environmental aspects can influence the activation and phenotype of immune cells. This data paper describes the gene expression levels in peripheral blood mononuclear cells (PBMCs) of multiparous sows, using RNA sequencing. Sows of various parity ranks were housed during gestation in a stable social group either in a conventional environment on a slatted concrete floor (C) or in an enriched environment with deep straw litter and a bigger space allowance (E). Videos were recorded between days 99 and 104 of gestation (G; G99 and G104) to determine the sows’ dominance status. Blood samples were collected at 98 days of gestation (G98) and 12 days of lactation (L12), and the PBMC fraction was isolated. Then, total RNA was extracted from PBMC and submitted to next-generation sequencing using the Illumina NextSeq 2000 system. Quality control, mapping, and annotation were performed using the Dragen RNA v3.8.4 software. The differential analysis was performed using the R package DESeq2. Differentially expressed genes (DEGs) were identified using a criterion of adjusted P-value (p-adj) cut-off <0.1 and fold-change >1.2 or <0.83 to identify up-regulated and down-regulated genes. For each time point (G98 and L12), the following contrasts were used for the differential analysis: sows housed in the enriched environment compared to the conventional environment [E vs C], dominant (Dom) sows compared to subordinate (Sub) sows [Dom vs Sub], and high parity sows (HP: 4th gestation or higher) compared to low parity sows (LP: 2nd and 3rd gestation) [HP vs LP]. The identified DEGs were used for functional analysis using the Database for Annotation, Visualisation, and Integrated Discovery software. To our knowledge, this is the first dataset allowing the investigation of the simultaneous effects of housing environment, dominance status, and parity on the PBMC transcriptome of adult sows. These data could also be used to compare the transcriptomes of pregnant and lactating females.