Chromatin supplement (combined draft; results/184/184_FigS_chromatin_combined; Fig. S8). Groups (RP genes excluded): Alu-near (classes 1 + 5), Alu-mid (2 + 3 + 6), Alu-far (4 + 7), L1/LTR CGI (8 + 9).
(A) Mean histone signal within TSS +/- 2.5 kb by expression tertile (Corces TPM within the cell type) in HPC, T cells and B cells (even-numbered autosomes); each row has its own y scale; open symbol, fewer than 30 genes; bars, gene-level 95% intervals (Data S2, Table 1b). Histone signal scales differ between cell types and are not compared across them.
(B) Methylation boundary by expression in T cells and B cells (the HPC version is Fig. 6B): Kaplan-Meier fraction of sides risen by distance from the TSS (rise = first 100-bp bin from the TSS with >= 2 non-repeat CpGs at >= 50% followed by an informative bin >= 50%; sides censored where informative CpGs end; CpGs overlapping RepeatMasker elements excluded; all autosomes; gene-clustered); expression tertiles bottom (light), middle, top; ticks, tertile KM medians; grey line, 0.5; thin line with n, fewer than 50 sides.
(C) CpG methylation measured from the TSS (top row, 0-2.5 kb) and outward from the island edge (bottom row, 0-2 kb) in HPC, T cells and B cells, Alu groups only (Alu-near, Alu-mid, Alu-far; L1/LTR CGI values in Data S2 / results/184/184_window_summary.csv); even-numbered autosomes; CpGs overlapping RepeatMasker elements excluded; 100-bp bins, gene value = mean of the upstream and downstream sides, mean over genes; bands, gene-level bootstrap 95% intervals (1,000 draws); grey line, 50%. Edge-referenced profiles are not truncated at the nearest retroelement.
