Chromatin accessibility assay

For the analysis of chromatin accessibility in multiple repetitive elements, 1 × 10⁶ CD15⁺ CD16⁺ neutrophils and 1 × 10⁶ CD3⁺ lymphocytes from four donors were subjected to chromatin extraction and nuclease digestion according to manufacturer's instructions (EpiQuik Chromatin Accessibility Assay kit, P-1047 Epigentek). Purified DNA was analyzed via real time qPCR using primers for different repeats (see Supplementary Table S1). Fold enrichment (FE) was calculated as the ratio of amplification efficiency (Ct) of the digested DNA sample over that of the non-digested sample. Large Ct shifts between digested and undigested samples, rendering high FE%, indicated that the target region was in the open chromatin, while minimal Ct shifts, resulting in low FE%, indicated that the target region was in the closed chromatin.