REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
E. coli DH5α	Vazyme	C502
BL21(DE3) Chemically Competent Cell	Transgen Biotech	CD601
Mouse hepatitis virus-A59	This study	N/A
Biological samples
Clinical samples	This study	Ethical number: 2022-168-01 (Nanjing Drum Tower Hospital)
Chemicals, peptides, and recombinant proteins
IPTG	Sangon Biotech Co.	A100487
TCEP	Sangon Biotech Co.	A600974
LB Broth	Sangon Biotech Co.	A507002
High Affinity Ni-NTA Resin	GenScript Biotech Co.	L00250
imidazole	Sangon Biotech Co.	A600277
RNA Clean & Concentrator-5 kit	Zymo Research	R1015
VAHTS DNA Clean Beads	Vazyme Biotech Co., Ltd.	N411
Ribo-off rRNA Depletion Kit (Human/Mouse/Rat)	Vazyme Biotech Co., Ltd.	N406
VAHTS RNA Clean Beads	Vazyme Biotech Co., Ltd.	N412
RNase H	New England BioLabs	M0297
DNase I	New England BioLabs	M0303
T4 RNA Ligase 1 (ssRNA Ligase)	New England BioLabs	M0204
T4 Polynucleotide Kinase (3' phosphatase minus)	New England BioLabs	M0236
NEBNext Multiplex Small RNA Library Prep Set for Illumina	New England BioLabs	E7580
RNA Fragmentation Reagents	Thermo Fischer Scientific	AM8740
Dulbecco's modified Eagle’s medium	Gibco	11995065
QIAzol Lysis Reagent	Qiagen	79306
Superior quality fetal bovine serum	Wisten	086
Agarose	Sangon Biotech Co.	A620014
Lipofectamine™ RNAiMAX Transfection Reagent	Invitrogen	13778100
ChamQ Universal SYBR qPCR Master Mix	Vazyme Biotech Co., Ltd.	Q711
HiScript II 1st Strand cDNA Synthesis Kit (+gDNA wiper)	Vazyme Biotech Co., Ltd.	R212
M-MLV (H-) Reverse Transcriptase	Vazyme Biotech Co., Ltd.	R021
RNase inhibitor	Vazyme Biotech Co., Ltd.	R301
dNTP Mix	Vazyme Biotech Co., Ltd.	P032
RNA Loading Dye (2X)	New England BioLabs	N0362
T7 High Yield RNA Transcription kit instructions	Vazyme Biotech Co., Ltd.	TR101
ClonExpress Ultra One Step Cloning Kit	Vazyme Biotech Co., Ltd.	C115
TRIzol Reagent	Invitrogen	15596026
IPTG	Sangon Biotech Co.	A100487
TCEP	Sangon Biotech Co.	A600974
LB Broth	Sangon Biotech Co.	A507002
High Affinity Ni-NTA Resin	GenScript Biotech Co.	L00250
imidazole	Sangon Biotech Co.	A600277
RNA Clean & Concentrator-5 kit	Zymo Research	R1015
VAHTS DNA Clean Beads	Vazyme Biotech Co., Ltd.	N411
Deposited data
NJU-seq for rRNA sites	This paper	SRR13333771, SRR13333776, SRR13333787 to SRR13333788
NJU-seq for mRNA sites	This paper	SRR13333772 to SRR13333775, SRR13333777 to SRR13333784, SRR13314941 to SRR13314946, SRR13314948, and SRR13314949
RNA-seq	This paper	SRR27559296 to SRR27559301
HeLa protein abundance data	PaxDb	Experiment ID 182
Experimental models: Cell lines
HeLa	Shanghai Institute of Cell Biology, Chinese Academy of Sciences	SCSP-504
HEK293T	Shanghai Institute of Cell Biology, Chinese Academy of Sciences	SCSP-502
A549	Shanghai Institute of Cell Biology, Chinese Academy of Sciences	SCSP-503
Neuro-2a	Shanghai Institute of Cell Biology, Chinese Academy of Sciences	SCSP-5035
Oligonucleotides
See Tables S5 and S6	This study	N/A
Software and algorithms
Cutadapt 2.10	Kechin et al.49	https://cutadapt.readthedocs.io/en/stable/
Bowtie 2 2.3.4	Langmead et al.50	https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Perl scripts	This paper	https://github.com/IvanWoo22/NJU_seq (https://doi.org/10.5281/zenodo.10572326)
R scripts	This paper	https://github.com/IvanWoo22/NJU_seq (https://doi.org/10.5281/zenodo.10572326)
ggseqlogo	Wagih et al.51	https://omarwagih.github.io/ggseqlogo/
PLEXY	Kehr et al.52	http://www.bioinf.uni-leipzig.de/Software/PLEXY/
DESeq2 1.30.1	Love et al.53	https://github.com/thelovelab/DESeq2
Image J 1.54h	Schneider et al.54	https://imagej.net/ij/
MaxQuant 1.6.1.0	Cox and Mann55	https://www.maxquant.org
PyMOL 2.4	Schrödinger et al.56	https://pymol.org/2/