Reagent or Resource	Source	Identifier
Antibodies
Rabbit, Anti-N6-methyladenosine antibody	Cell Signaling Technology	Cat# 15000BC
Anti-rabbit IgG, HRP-linked antibody	Cell Signaling Technology	Cat# 7074S; RRID: AB_2099233
Mouse, Anti-CD14 antibody, RMO52	Beckman Coulter	Cat# IM0643
Monoclonal mouse, Anti-CD34 antibody, clone 8G12	BD Biosciences	Cat# 348050; RRID: AB_400369
Goat anti-Mouse IgG1 Cross-Adsorbed Secondary Antibody, Alexa Fluor 546	ThermoFisher	Cat# A-21123; RRID: AB_2535765
Goat anti-Mouse IgG2a Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	ThermoFisher	Cat# A-21241; RRID: AB_2535810
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, APC	ThermoFisher	Cat# A-10931; RRID: AB_2534068
Rabbit anti-PCIF1 Antibody	Bethyl Laboratories	Cat# A304-711A; RRID: AB_2620906
Rabbit anti-METTL3/MT-A70 Antibody	Bethyl Laboratories	Cat# A301-567A; RRID: AB_1040004
Chemicals, peptides, and recombinant proteins
3-(2-aminoethylamino)-propyltrimethoxysilane	Tokyo Chemical Industry Co.	Cat# A0774
Acetic acid	Sigma	Cat# A6283
Azide PEG Succinimidyl Carboxymethyl Ester	JenKem Technology USA Inc.	Cat# A5088-1
Dimethyl sulfoxide, anhydrous, ≥99.9%	Sigma	Cat# 276855
Triethylamine	Sigma	Cat# 471283
Copper(II) sulfate pentahydrate	Sigma	Cat# 209198
Tris-hydroxypropyltriazolylmethylamine (THPTA)	Click Chemistry Tools	Cat# 1010-100
Sodium ascorbate	Sigma	Cat# A4034
N6-methyladenosine-5’-triphosphate	TriLink	Cat# N1013
1 M MgCl2	Sigma	Cat# 63069-100ML
1 M Tris-HCl pH 8.0	Boston BioProducts	Cat# BBT-80
10 mM dNTPs	New England BioLabs	Cat# N0447L
BSA	Sigma	Cat# A9418-100G
RNase Inhibitor	Thermo Fisher	Cat# AM2696
Tween-20	Fisher Scientific	Cat# 65-520-4100ML
UltraPure™ 0.5M EDTA, pH 8.0	Invitrogen	Cat# 15575020
Sodium Chloride	Fisher Chemical	Cat# S671-3
Potassium hydroxide	Sigma	Cat# P5958
10% NP-40	Abcam	Cat# ab142227
pCp-Cy3	Jena Bioscience	Cat# NU-1706-CY3
Protocatechuate 3,4-Dioxygenase	Sigma	Cat# P8279-25UN
Protocatechuic acid	Sigma	Cat# P5630
Trolox	Sigma	Cat# 238813
Amersham Hybond-XL	Cytiva	Cat# RPN303s
Cyanine 3-dATP	PerkinElmer	Cat# NEL592001EA
1X ThermoPol buffer	New England BioLabs	Cat# B9004S
Virtual terminator dNTP analogs	SeqLL	N/A
Adenosine	Toronto Research Chemicals	Cat# A280400
2'-Deoxyadenosine Monohydrate	Toronto Research Chemicals	Cat# D231620
N6-Methyladenosine	Toronto Research Chemicals	Cat# M275895
N6,O2'-Dimethyladenosine	Toronto Research Chemicals	Cat# D447415
Hoechst 33342	Invitrogen	Cat# 62249
SYTO9	Invitrogen	Cat# S34854
SYTO87	Invitrogen	Cat# S11363
Hybridization Chamber Kit - SureHyb enabled	Agilent	Cat# G2534A
FluoSphere beads	Thermo Fischer	Cat# F8807
Azido-PEG3-SS-NHS	Conju Probe	Cat# CP-2060
AFDye 647 DBCO	Click Chemistry Tools	Cat# 1302-1
Azide Magnetic Beads	Click Chemistry Tools	Cat# 1036-1
20X SSC	Thermo Fischer	Cat# 15557036
Formamide	Sigma	Cat# F9037
Dextran Sulfate	Sigma	Cat# D8906; D4911
TCEP	Sigma	Cat# 646547
Critical commercial assays
HiScribe™ T7 Quick High Yield RNA Synthesis Kit	New England BioLabs	Cat# E2050
RNAClean XP Kit	Beckman Coulter	Cat# A66514
E. coli Poly(A) Polymerase	New England BioLabs	Cat# M0276
T4 RNA Ligase 1	New England BioLabs	Cat# M0204
Dynabeads mRNA DIRECT Purification Kit	Invitrogen	Cat# 61011
Pierce™ ECL Western Blotting Substrate	Thermo Fisher	Cat# 32106
RNeasy Mini Kit	QIAGEN	Cat# 74104
Klenow Fragment (3’→5’ exo-)	New England BioLabs	Cat# M0212S
Proteinase K	New England BioLabs	Cat# P8107S
SuperScript III Reverse Transcriptase	Invitrogen	Cat# 18080093
Exonuclease I	New England BioLabs	Cat# M0293S
Terminal Transferase	New England BioLabs	Cat# M0315S
RppH	New England BioLabs	Cat# M0356S
RNA Clean and Concentrator-5 Kit	Zymo Research	Cat# R1013
Nuclease P1	New England BioLabs	Cat# M0660
Shrimp Alkaline Phosphatase	New England BioLabs	Cat# M3071S
YM-10 centrifugal spin column	Millipore	Cat# MRCPRT010
Illustra NAP-5 columns	GE Healthcare	Cat# 17-0853-01
Deposited Data
m6A-LAIC-seq	Molinie et al., 2016	GSE66086
Experimental models: Cell lines
K562	ATCC	Cat# CCL-243
YAC1	ATCC	Cat# TIB-160
GM12878	Coriell	Cat# GM12878
MUTZ3	DSMZ	Cat# ACC-295
5637	ATCC	Cat# HTB-9
Oligonucleotides
in vitro-generated transcripts (IVTs)	Integrated DNA Technologies	5’-GGCCAGTGAATTGTAATACGACTC ACTATAGGGAGGCGGTAACACCTTC TGGACTCTTCATAGAGTTGGTCTATT TGTCTCCACGCTGCCAGGTTGTTGT GGCCTGTTTTCGGGCGTCTGCGGC GAAGATCTCTTGTCAGAGCCTTAGG TGTATCTAGATTGTGATCCCCTTTCC TCACTTGGTAGTCTGTCGACTT-3’
Hexynyl-Oligo dT50	Integrated DNA Technologies	5’Hexynyl-TTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3’
Synthetic RNA fragments	Integrated DNA Technologies	rArC-rX-rUrG, X=A, m6A, U or ψ
METTL3 gRNA_1	Integrated DNA Technologies	5’-ATCATTCGGACAGGCCGTAC-3’
METTL3 gRNA_2	Integrated DNA Technologies	5’-GCTCAACATACCCGTACTAC-3’
PCIF1 gRNA_1	Integrated DNA Technologies	5’-GATCCGTTTGACGTACTCCA -3’
PCIF1 gRNA_2	Integrated DNA Technologies	5’-ACTTAACATATCCTGCGGGG-3’
Control gRNA_1	Integrated DNA Technologies	5’-ACGGAGGCTAAGCGTCGCAA-3’
Control gRNA_2	Integrated DNA Technologies	5’-CGCTTCCGCGGCCCGTTCAA-3’
seqFISH probes	Integrated DNA Technologies	See the Table S2
Recombinant DNA
pGIR-PB-U6-NT1(H.s)-CMV-Cas9-T2a-eGFP	Table S3	N/A
pGIR-PB-U6-NT2(H.s)-CMV-Cas9-T2a-eGFP	Table S3	N/A
pGIR-PB-U6-METTL3-gRNA1-CMV-Cas9-T2a-eGFP	Table S3	N/A
pGIR-PB-U6-METTL3-gRNA2-CMV-Cas9-T2a-eGFP	Table S3	N/A
pGIR-PB-U6-PCIF1-gRNA1-CMV-Cas9-T2a-eGFP	Table S3	N/A
pGIR-PB-U6-PCIF1-gRNA2-CMV-Cas9-T2a-eGFP	Table S3	N/A
Software and algorithms
Scripts used for image processing and single-cell analysis	This paper	https://github.com/Kim-KL/scRNAmod
R version 3.4	R Core Team	https://www.r-project.org
ImageJ 1.46 r	NIH	https://imagej.nih.gov/ij/