Extended Data Fig. 2: RNA-seq and ATAC-seq analysis for ERVs in non-senescent and senescent WI38, IMR90, and BJ cells.
a, Scatterplot representing differences in ERVs expression in non-senescent and senescent BJ cells by RNA-seq analysis. Red dots indicate ERV elements with significantly increased expression, while blue dots indicate ERV elements with significantly decreased expression. b, Regression analysis of the correlation for the log2FoldChange (senescent versus non-senescent) of ERV elements expression between WI38 and BJ cells. R is Pearson correlation coefficient. P value was calculated using a two-sided Pearson’s correlation test. c, The profiles for genomic regions of ERV1, ERVK, ERVL, and ERVL-MaLR subfamilies by ATAC-seq analysis in BJ cells. d, Heatmap showing expression by RNA-seq analysis (left) and chromatin accessibility by ATAC-seq analysis (right) of ERV elements in non-senescent and senescent BJ cells. e, Venn diagram showing the overlap of significantly activated ERV elements in senescent WI38, IMR90, and BJ cells. f, log2FoldChange differences of chromatin accessibility (left) and expression (right) of LTR39, MER61C, MER61-int, MSTC, and MST-int, between senescent and non-senescent BJ cells, revealed by ATAC-seq and RNA-seq respectively. g, Signal distributions of ATAC-seq and RNA-seq at the representative genomic loci of LTR39, MER61C, MER61-int, MSTC, and MST-int, in non-senescent and senescent BJ cells. P values were calculated by Wald test in DESeq2 (a and f). non-Sen, non-senescent. Sen, senescent.
