Additional file 5 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

Additional file 5: Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis. A. Whole-lung (WL) tissue - SQuIRE, B. Alveolar type II (AT2) cells - SQuIRE. C. Alveolar macrophages (AM) - SQuIRE. D. Whole-lung (WL) tissue - REdiscoverTE, E. Alveolar type II (AT2) cells - REdiscoverTE. F. Alveolar macrophages (AM) - REdiscoverTE. The columns represent the repeat classification, the TE expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value). Only significant upregulated families are shown. G. Summary of all changes in REdiscoverTE analysis.