Whole transcriptome data of primary human NK cells under hypoxia and interleukin 15 priming: A 2×2 factorial design experiment

Abstract

Natural Killer (NK) cells mediate innate immunity against cancer and intracellular infection, at that, operating in often oxygen-deprived environments. We performed a microarray experiment with a 2×2 factorial design to profile gene expression in human NK cells (Velasquez et al., 2016) [1]. In this experiment, NK cells from 5 healthy volunteers were primed or not for 6 h with the survival factor and inflammatory cytokine interleukin 15 (IL-15) under hypoxic or normoxic culture conditions (20 samples in total). Here, we provide details on the culture setup that govern the actual O₂ partial pressure (pO₂) experienced by the cells, as well as on the RNA extraction procedure used, which we optimized from commercial spin column protocols to obtain highly concentrated total RNA. We present a quality control analysis of the normalized microarray data, as well as overviews for differentially regulated genes. These data provide insights into NK cell transcriptional responses to immune stimulation under physiologically relevant low oxygen conditions. This dataset is deposited in the Gene Expression Omnibus database (accession number GSE70214).

Keywords: Hypoxia; Interleukin 15; Microarray; Natural Killer cells.

Fig. 1

Boxplots for signal intensity distributions of arrays from all donors and experimental conditions after normalization. Experimental conditions are abbreviated as follows: H and N stand for normoxia and hypoxia without priming, respectively, and +IL-15 indicates priming under either condition.

Fig. 2

Venn diagram of the significant genes (FDR<0.05) that are differentially expressed for each group. H and N stand for normoxia and hypoxia without priming, respectively, and +IL-15 indicates priming under either condition.

Fig. 3

Heatmap of genes significantly regulated by hypoxia and IL-15 priming. H and N stand for normoxia and hypoxia without priming, respectively, and +IL-15 indicates priming under either condition.

Fig. 4

Heatmap of top 10 genes up- or down-regulated by either experimental condition, IL-15 priming (+IL-15) and hypoxia (H) from Fig. 3. N stands for normoxia. Fold changes (FC) for 4 comparisons are displayed as dark orange–green heatmap. Red–blue heatmaps represent normalized intensities. Notably, donor 1 shows high intensities for several TRAJ (T cell receptor alpha joining) genes under hypoxia without IL-15 priming.