| 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
|
