REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
J2 monoclonal antibody, mouse, IgG2a, Kappa chain, 100×	SCICONS	Cat# 10010200; RRID: AB_2651015
Donkey mouse IgG (H+L) secondary antibody, Alex Fluor 555, 1,000×	Invitrogen	Cat# A-31570; RRID: AB_2536180
Chemicals, peptides, and recombinant proteins
TRIzol reagent	Invitrogen	Cat# 10296028
Recombinant DNase I (RNase-free)	TaKaRa	Cat# 2270
SuperScript IV Reverse Transcriptase	Invitrogen	Cat# 18090200
Paraformaldehyde	Sigma	Cat# P6148; CAS: 30525-89-4
Triton X-100, molecular biology grade	Promega	Cat# H5141
Bovine serum albumin (BSA)	RMBIO	Cat# BSA-BSH
4′,6-Diamidino-2-phenylindole, dihydrochloride (DAPI)	Invitrogen	Cat# D1306; CAS: 28718-90-3
MitoGreen	PromoKine	Cat# PK-CA707-70054
Chloroform	Sigma	Cat# 496189
Acid-phenol:chloroform, pH 4.5	Invitrogen	Cat# AM9722
3 M Sodium acetate, pH 5.5	Invitrogen	Cat# AM9740
GlycoBlue Coprecipitant (15 mg/mL)	Invitrogen	Cat# AM9516
Recombinant RNase Inhibitor (40 U/μL)	TaKaRa	Cat# 2313A
SensiFAST SYBR Lo-Rox Kit	Bioline	Cat# BIO-94020
dNTP mmixture (2.5 mM)	TaKaRa	Cat# 4030
Dithiothreitol (DTT)	VWR Chemicals	Cat# 0281
Gelatin, type A	MP Biomedicals	Cat# 901771
Ethanol, absolute	Alfa Aesar	Cat# A9951
Isopropanol	Merck	Cat# 8.18766
Critical commercial assays
RNAscope Multiplex Fluorescent V2 Assay	ACD	N/A
Deposited data
Unprocessed microscopy data deposited to Mendeley Data	This paper	https://doi.org/10.17632/3r7r9r2n6t.2; https://data.mendeley.com/drafts/3r7r9r2n6t
Experimental models: Cell lines
SW1353	ATCC	Cat# HTB-94; RRID: CVCL_0543
HEK293T	ATCC	Cat# CRL-3216; RRID: CVCL_0063
NS-SV-AC		RRID: CVCL_UD37
Oligonucleotides
See Table S1 for the List of tag for strand-specific RT-qPCR	This paper	https://doi.org/10.17632/3r7r9r2n6t.2; https://data.mendeley.com/drafts/3r7r9r2n6t
See Table S2 for the List of primers for strand-specific reverse transcription	This paper	https://doi.org/10.17632/3r7r9r2n6t.2; https://data.mendeley.com/drafts/3r7r9r2n6t
See Table S3 for the List of primers for strand-specific qPCR	This paper	https://doi.org/10.17632/3r7r9r2n6t.2; https://data.mendeley.com/drafts/3r7r9r2n6t
Software and algorithms
ImageJ	ImageJ	https://imagej.nih.gov/ij/
Illustrator	Adobe	N/A
Other
Dulbecco’s modified eagle medium (DMEM; High-glucose, with 4 mM L-glutamine, 100 mg/L sodium pyruvate, and 3,700 mg/L sodium bicarbonate)	Welgene	Cat# LM001-05
Phosphate buffered saline (PBS) Tablets	TaKaRa	Cat# T9181
Qualified fetal bovine serum (FBS)	Gibco	Cat# 26140079
Trypsin-EDTA	Welgene	Cat# LS015-01
G-Tube Flat Top Microcentrifuge Tube, Natural	Bio Plas	Cat# 4030
1.7 mL microcentrifuge tube	Axygen	Cat# MCT-175-C
AriaMx Real-time PCR system	Agilent	N/A
QuantStudio 1 Real-time PCR system	Thermo Scientific	N/A
HybEZ II Oven System	ACDBio	N/A
Eppendorf BioPhotometer D30	Eppendorf	N/A
Confocal dish	SPL	Cat# 101350
8-chamber slide	Thermo Scientific	Cat# 154534PK
60-mm dish	SPL	Cat# 20060
100-mm dish	SPL	Cat# 20100
6-well plate	SPL	Cat# 30006
0.22 μm filter	Merck	Cat# SLGP033RB
15 mL conical tube	SPL	Cat# 50015
MicroAmp 96-well plate	Thermo Scientific	Cat# N8010560
MicroAmp optical adhesive film	Thermo Scientific	Cat# 4311971