Nucleolar and PCH TSA-Seq was performed using either Condition C (labeling with 1:3000 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) or Condition E (labeling with 1:300 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) with the following minor modification: 150ul of Dynabeads M-270 streptavidin (Invitrogen, catalog no. 65306) was used to purify the biotinylated DNA. LMNB1 TSA-seq was performed using Condition AI for HFFc6, H1, and K562 and Condition A for HCT116 cells. POL1RE and MKI67IP TSA-Seq, raw sequencing reads were mapped to the Telomere-to-Telomere (version 1.1).