REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-N6-methyladenosine (m6A)	EMD Millipore	ABE572-I, RRID:AB_2892214
Anti-rabbit IgG, HRP-linked Antibody	Cell signaling technology	7074, RRID:AB_2099233
Chemicals, peptides, and recombinant proteins
D5000 ScreenTape	Agilent	5067-5588
D5000 Reagents	Agilent	5067-5589
SAM (32-mM)	NEB	B9003S
Water (nuclease free)	Ambion	AM9932
1 M Tris, pH 8.0 (nuclease free)	Invitrogen	AM9855G
5 M NaCl (nuclease free)	Invitrogen	AM9760G
2 M KCl (nuclease free)	Invitrogen	AM9640
0.5 M EDTA pH 8.0	Invitrogen	AM9260G
0.5 M EGTA, pH 8.0	Alfa Aesar	J60767-AE
Spermidine, 5 M	Sigma	85558-5G
10% Triton X-100 (nuclease free)	Sigma	93443-100ml
rBSA	EMD Millipore	126609-10GM
Genomic DNA ScreenTape	Agilent Technologies	5067-5365
HisTrap HP	Cytiva	17524802
Streptavidin Coated 96-well ELISA plate	Thermo scientific	15124
Ultra TMP-ELISA substrate	Thermo scientific	34028
Critical commercial assays
SMRTBELL prep kit 3.0	Pacific Biosciences	102-141-700
SMRTBELL barcoded adapter plate	Pacific Biosciences	102-009-200
AMPure PB beads	Pacific Biosciences	100-265-900
Chromium GEM-X Single Cell 3' Kit v4 16 rxns	10x Genomics	1000691
Chromium GEM-X Single Cell 3' Chip Kit v4 4 chips	10x Genomics	1000690
Dual Index Kit TT Set A 96 rxns	10x Genomics	1000215
KAPA Library Quantification Kit Illumina® Platforms	Roche	KK4828 – 07960166001
Megaruptor 3 DNAFluid kit	Diagenode	E07020001
Megaruptor 3 Shearing kit	Diagenode	E07010003
Monarch Genomic DNA kit	New England Biolabs	T3010L
Software and algorithms
Python	Python Software Foundation	https://www.python.org/
Visual Studio Code	Microsoft	https://visualstudio.microsoft.com/
Adobe Illustrator	Adobe Inc.	https://www.adobe.com/products/illustrator.html
Fibertools	Stergachis Lab	https://github.com/fiberseq/fibertools-rs
R	R Core Team	https://www.r-project.org/
Numpy	Numpy Team	https://numpy.org/
Pandas	NumFOCUS Inc.	https://pandas.pydata.org/
Matplotlib	Matplotlib Development Team	https://matplotlib.org/
Seaborn	Michael Waskom	https://seaborn.pydata.org/
Scipy	Scipy Steering Council	https://scipy.org/
Pyft	Stergachis Lab	https://py-ft.readthedocs.io/en/latest/
Deposited data
Fiber-seq and single nuclei sequencing data	This paper	dbGAP: phs003771.v1.p1