REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-N6-methyladenosine	Synaptic System	Cat# 202 003
Anti-V5	Cell Signaling	Cat# 13202; RRID:AB_2687461
Anti-Lamin A/C	Santa Cruz Biot.	Cat# sc-7292; RRID:AB_627875
Anti-TRF2	Abcam	Cat# ab13579; RRID:AB_300474
Anti-CREST	Immunovision	Cat# HCT-0100; RRID:AB_2744669
Telomere TelC-647	Panagene INC.	F2003
Centromere CEN-488	Panagene INC.	F3012
Bacterial and Virus Strains
E.Coli K-12 MG1655 – F-, λ-, rph-1	Yoshiharu Yamaichi, I2BC	N/A
E.Coli K-12 ER2925 – F-, ara-14, leuB6, fhuA31, lacY1, tsx78, glnV44, galK2, galT22, mcrA, dcm-6, hisG4, rfbD1, R(zgb210::Tn10)TetS, endA1, rpsL136, dam13::Tn9, xylA-5, mtl-1, thi-1, mcrB1, hsdR2	Yoshiharu Yamaichi, I2BC	N/A
E.Coli K-12 ER2796 – F-, fhuA2::IS2, glnX44(AS), λ-, e14-, trp-31, dcm-6, yedZ3069::Tn10, hisG1, argG6, rpsL104, Δdam-16::KanR, xyl-7, mtlA2, metB1, Δ(mcrC-mrr)114:IS10	Yoshiharu Yamaichi, I2BC	N/A
Chemicals, Peptides, and Recombinant Proteins
Shield	Aobious	Cat# AOB1848
Thymidine	Sigma	Cat# T1895
2-Deoxycytidine	Sigma	Cat# D3897
Critical Commercial Assays
QIAGEN Blood & Cell Culture DNA Midi Kit	QIAGEN	Cat# 13323
Dynabeads streptavidin	Invitrogen	Cat# M280
Next End-repair module	NEB	Cat# E6050
Next A-tailing module	NEB	Cat# E6053
Next Ligation Module	NEB	Cat# E6056
Gibson Assembly Cloning kit	NEB	Cat# E5510
Deposited Data
Raw data (MadID)	This paper	ArrayExpress: E-MTAB-6888
DamID microarrays	Kind et al., 2013	GEO GSM990672 and GSM990672
Single-cell DamID	Kind et al., 2015	GEO GSE68263
Mendeley dataset	This paper	https://doi.org/10.17632/8j9kmzm4bc.1
Experimental Models: Cell Lines
IMR90	ATCC	Cat# CCL-186; RRID:CVCL_0347
U2OS	ATCC	Cat# 300364/p489_U-2_OS; RRID:CVCL_0042
HeLa 1.2.11	Crabbe et al., 2012	N/A
Oligonucleotides
Cloning M.EcoGII pLPC	This paper	N/A
FW GCGGATCCATGCTTAATACTGTAAAAATATC
REV GCGAATTCAACGATTAAATCCTGAACTTC
Cloning M.EcoGII pRetroXPTuner C-tag	This paper	N/A
FW CGGGATCCGGTAAGCCTATCCCTAACCCTCTCCT CGGTCTCGATTCTACGCGTACCGGCATGCTTAATAC TGTAAAAATATCC
REV CGGCGGCCGCTTAAACGATTAAATCCTGAACTTC
Cloning M.EcoGII pRetroXPTuner N-tag	This paper	N/A
FW CGGGATCCGTATGCTTAATACTGTAAAAATATCC
REV CGCCATGGAACGATTAAATCCTGAACTTC
Q-PCR primer CFHR3	Kind et al., 2013	N/A
FW TTGGAAGAAGAGAAAGACAAGG
REV GCAGTGGATGTTTCTCAGCA
Q-PCR primer CYP2C19	Kind et al., 2013	N/A
FW GGATGAGCTTTGCAGGAGAT
REV AAGCTGTGAGCCTGAGCAGT
Q-PCR primer CDH12	Kind et al., 2013	N/A
FW TTTTTCCTCCCAGGTGACAG
REV TGATAGCACCTGGGTTAGCAC
Q-PCR primer LAD1	Kind et al., 2013	N/A
FW CATTGGCTTCTTTGGTGCCAGGT
REV ACGGTGGAGGCAGTCAAAAGGC
Q-PCR primer iLAD1	Kind et al., 2013	N/A
FW GAAGGTTCCCCCACAGAAAT
REV CTGAGGCAAAGACAGGGAAG
Q-PCR primer UBE2B	Kind et al., 2013	N/A
FW ACTCAGGGGTGGATTGTTGA
REV GCCAGAGATTTCAGGGAAAG
Q-PCR primer STAG2	Kind et al., 2013	N/A
FW GCATTTGGATGCCTTATTGC
REV GAACATGCTTCCAAAACATCTG
Recombinant DNA
pLPC-hTERT	Titia de Lange, Rockefeller University	N/A
PRRS GII – M.EcoGII	Yoshiharu Yamaichi, I2BC	N/A
pRetroX-PTuner DD-linker-M.EcoGII	This paper	N/A
pRetroX-PTuner DD-linker-M.EcoGII-v5-Lamin B1	This paper	N/A
pRetroX-PTuner DD-M.EcoGII-v5-Telomeric repeat-binding factor 1	This paper	N/A
pRetroX-PTuner DD-M.EcoGII-v5-Centromeric protein C	This paper	N/A
Software and Algorithms
bcl2fastq2 V2.15.0	N/A	N/A
Bwa	N/A	http://bio-bwa.sourceforge.net
Samtools	N/A	http://www.htslib.org/
Bedtools	N/A	https://bedtools.readthedocs.io/en/latest/