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. Author manuscript; available in PMC: 2024 Nov 2.
Published in final edited form as: Mol Cell. 2023 Oct 10;83(21):3818–3834.e7. doi: 10.1016/j.molcel.2023.09.020

KEY RESOURCES TABLE.

REAGENTor RESOURCE SOURCE IDENTIFIER

Antibodies

m6A Synaptic systerms Cat#202003; RRID:AB_2279214
METTL3 ABClonal Cat#A21572
ALKBH5 Sigma Cat#HPA007196; RRID:AB_1850461
FTO Sigma Cat#SAB2106776
METTL16 ABClonal Cat#A15894; RRID:AB_2763325
CDK9 ABClonal Cat#A11145; RRID:AB_2861506
RNAP II Abcam Cat#ab300575
Ser2P Abcam Cat#ab238146
HA Abcam Cat#ab9110; RRID:AB_307019
Flag Sigma Cat#F7425; RRID:AB_439687
Actin Proteintech Cat#60008-1-Ig; RRID:AB_2289225
Alexa Fluor 488 AffiniPure Goat Anti-Mouse IgG Jackson ImmunoResearch Cat#115-545-003; RRID: AB_2338840
Alexa Fluor 594 AffiniPure Goat Anti-Rabbit IgG Jackson ImmunoResearch Cat#111-585-003; RRID: AB_2338059
MePCE Proteintech Cat#14917-1-AP; RRID:AB_2250635
Larp7 Proteintech Cat#17067-1-AP; RRID:AB_2132693
HEXIM1 Proteintech Cat#15676-1-AP; RRID:AB_2248363
CyclinT 1 Cell Singnal Cat#81464; RRID:AB_2799973
H3 Sigma Cat# H0164; RRID: AB_532248
hnRNPA2/B1 Santa Cruz Cat#sc-374053; RRID:AB_10947257

Chemicals, peptides, and recombinant proteins

Lipofectamine 3000 Invitrogen Cat# L3000015
Streptavidin Dynabeads Thermo Fisher Cat# 65002
TRIzol reagent Thermo Fisher Cat# 15596018
Dynabeads Protein G Thermo Fisher Cat# 88848
Proteinase K VWR Cat# 97062-238
Protease Inhibitor Cocktail Sigma Cat# 5056489001
MTSEA BIOTIN Biotium Cat# 90066
4-THIOURIDINE Sigma Cat# T4509
NAI Millipore Cat# 03-310
SsoAdvanced Universal SYBR Green Supermix Biorad Cat# 1725274
Glycoblue Coprecipitant Thermo Fisher Cat# AM9516
Potassium Chloride Affymetrix Cat# 75896
Dynabeads M-280 Sheep anti-Rabbit IgG Thermo Fisher Cat# 11204D

Critical commercial assays

Qubit 1X dsDNA HS Assay Kit Invitrogen Cat# Q33230
Qubit RNA HS assay Kit Invitrogen Cat# Q32852
TURBO DNA-free Kit Invitrogen Cat# AM1907
Smart Stranded Total RNA-Seq Kit v3 Takara Cat# 634488
ThruPLEX Tag-seq 96D Kit Takara Cat# R400586
SuperScript II Reverse Transcriptase Invitrogen Cat# 18064014
iClick EU Andy Fluor 594 Imaging Kit ABP Biosciences Cat# A010
QuantiTect Reverse Transcription Kit QIAGEN Cat# 205313
Agencourt RNAclean XP beads Beckman Coulter Cat# A63881
Protein Assay Reagent S Bio-Rad Cat# 5000115
Protein Assay Reagent A Bio-Rad Cat# 5000113

Deposited data

The raw and processed sequencing data This paper SRA: PRJNA938517

Experimental models: Cell lines

HEK293T Laboratory of Joan A. Steitz N/A
A549 Laboratory of Lingtao Jin N/A
BEAS-2B Laboratory of Lizi Wu N/A
MRC-5 Laboratory of Lizi Wu N/A
H2009 Laboratory of Lizi Wu N/A
H23 Laboratory of Lizi Wu N/A
H1299 Laboratory of Lizi Wu N/A

Oligonucleotides

RT-qPCR primer sequences This paper See Table S1
Northern blot probe sequences This paper See Table S2
siRNA sequences This paper See Table S3
SELECT primer sequences This paper See Table S4
DNA oligonucleotides for RNase H This paper See Table S5
7SK SLI sequences This paper See Table S6
Primer sequences for SHAPE-MaP library This paper See Table S7

Recombinant DNA

pMSCV-dCasRx-ALKBH5 Addgene 175582
pMSCV-dCasRx-ALKBH5 H204A This paper N/A
pCDNA3.1-Flag-ALKBH5 This paper N/A
pCDNA3.1-Flag-ALKBH5 H204A This paper N/A
pCDNA3.1-Flag-METTL3 This paper N/A
pCDNA3.1-Flag-METTL3 D395A This paper N/A

Software and algorithms

Prism 9 Gaphpad Software https://www.graphpad.com/scrientifificsofware/prism/
Custom sequencing analysis scripts This paper https://doi.org/10.5281/zenodo.8341420
FastQC program Babraham Bioinformatics bioinformatics.babraham.ac.uk/projects/fastqc/
Trimmomatic Bolger et al.86 N/A
PEAR Zhang et al.87 N/A
cutadapt Martin88 N/A
HISAT2 Kim et al.89 N/A
Samtools Li et al.90 N/A
HTSeq Anders et al.91 N/A
Plotly Inc., P.T.92 N/A
DeepTools Huang et al.93 N/A
MACS2 callpeak Rami´rez et al.94 N/A
HISAT-3N Zhang et al.95 N/A
deltaSHAPE.py Laboratory of Kevin M. Weeks weekslab.com/software
StructureEditorv6.2 Laboratory of David H. Mathews rna.urmc.rochester.edu/GUI/html/StructureEditor.html