REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse Anti-RNA Polymerase II H5 monoclonal antibody, Unconjugated (1:100 IF)	Covance	Cat# MMS-129R; RRID: AB_10143905
Goat anti-Mouse IgM (Heavy chain) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (1:2,000 IF)	Thermo Fisher Scientific	Cat# A-21042; RRID: AB_2535711
Chemicals, peptides, and recombinant proteins
Demecolcine	Sigma-Aldrich	Cat# D7385
α-amanitin	Merck	Cat# A2263-1MG
Retinoic acid	Merck	Cat# R2625-50MG
Tyrode’s Solution	Sigma-Aldrich	Cat# T1788
G-MEM with L-Glutamine and Phenol Red	Wako	Cat# 078-05525
DMEM, high glucose, GlutaMAX™ Supplement	Thermo Fisher Scientific	Cat# 10566016
KnockOut Serum Replacement	Thermo Fisher Scientific	Cat# 10828028
Fetal Bovine Serum	Cosmo Bio/Funakoshi	Cat# S-FBS-NL-015/ S1820
Stemolecule CHIR99021	REPROCELL	Cat# 04-0004
Stemolecule PD0325901	REPROCELL	Cat# 04-0006
Sodium Pyruvate	Thermo Fisher Scientific	Cat# 11360-070
2-Mercaptoethanol	Merck	Cat# M3148-100ML
Non-essential amino acids	Thermo Fisher Scientific	Cat# 11140-050
Leukemia Inhibitory Factor Protein, Recombinant mouse	Merck Millipore	Cat# LIF2010
Penicillin G Potassium Salt	Nacalai	Cat# 26239-84
Streptomycin Sulfate	Nacalai	Cat# 32237-14
Amphotericin B Suspension (Fungizone)	FUJIFILM	Cat# 019-23891
KSOMaa medium	ARK Resource	N/A
M2 medium	ARK Resource	N/A
HTF medium	ARK Resource	N/A
Mineral oil	Merck	Cat# M8410-1L
Liquid paraffin	Nacalai Tesque	Cat# 26137-85
Bovine serum albumin	Merck	Cat# A3311-50G
PBS	Thermo Fisher Scientific	Cat# 10010049
Hyaluronidase from bovine testes	Merck	Cat# H3884-100MG
Trypsin-EDTA solution	Merck	Cat# T4049-100ML
Pregnant mare serum gonadotrophin (PMSG)	ASKA Pharmaceutical Co.	Cat# 879412
Human chorionic gonadotropin (hCG)	ASKA Pharmaceutical Co.	Cat# 8772413
GenomeONE™-CF, Hemagglutinating virus of Japan envelope (HVJ-E) solution	ISHIHARA SANGYO KAISHA	Cat# CF004
VECTASHIELD Mounting Medium with DAPI	Funakoshi	Cat# H-1200
Pierce™ 16% Formaldehyde (w/v), Methanol-free	Thermo Fisher Scientific	Cat# 28906
Critical commercial assays
PicoPure™ RNA Isolation Kit	Thermo Fisher Scientific	Cat# KIT0204
SMART-seq v4 Ultra Low Input RNA Kit	Takara	Cat# 24888N
Nextera DNA Sample Preparation Kit	Illumina	Cat# FC-131-1024
mMESSAGE mMACHINE® SP6 Transcription Kit	Thermo Fisher Scientific	Cat# AM1340
Poly(A) Tailing Kit	Thermo Fisher Scientific	Cat# AM1350
Deposited data
RNA-seq	Tomikawa et al., 2021	GEO: GSE162345
Experimental models: Cell lines
Mouse ES cell line; NeoR5	Miyamoto et al., 2011	N/A
Mouse C2C12 cell line	Miyamoto et al., 2011	N/A
Oryx dammah cell	Tomikawa et al., 2021	N/A
Experimental models: Organisms/strains
C57BL/6 mice, female, 8 wk∼	CLEA Japan (Tokyo, Japan)	N/A
DBA/2 mice, male, 8 wk∼	CLEA Japan (Tokyo, Japan)	N/A
Oligonucleotides
LacR-mCherry mRNA	Miyamoto et al., 2011	N/A
Recombinant DNA
pCS2-LacR-mCherry vector	Miyamoto et al., 2011	N/A
Software and algorithms
ZEN	Carl Zeiss	N/A
Trimmomatic	Bolger et al., 2014	http://www.usadellab.org/cms/?page=trimmomatic
trim_galore 0.4.2	Babraham institute	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
cutadapt 3.1	Martin, 2011	https://cutadapt.readthedocs.io/en/stable/
STAR 2.5.4b	Dobin et al., 2013	https://github.com/alexdobin/STAR
DESeq2 1.22.2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Kallisto software 0.45.0	Bray et al., 2016	https://github.com/pachterlab/kallisto/releases
Sleuth 0.30.0	Pimentel et al., 2017	https://github.com/pachterlab/sleuth
Homer	Heinz et al., 2010	http://homer.ucsd.edu/homer/
Bedtools v2.26.0	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
deepTools 3.1.3	Ramírez et al., 2016	https://deeptools.readthedocs.io/en/develop/
Custom Source Code	Github Folder:s Miyamoto-lab/NT-ETR	https://github.com/Miyamoto-lab/NT-ETR; https://doi.org/10.5281/zenodo.5547988
Other
XYClone laser system	Hamilton Thorne	Cat# 271348
Flaming/Brown Micropipette Puller	Sutter Instrument	Cat# P-97
EM MYSTAR Hematocrit Capillary Plain Type	AS ONE	Cat# 2-454-20
Microforge	NARISHIGE	Cat# MF-900
Microinjector	Eppendorf	Product name: Femtojet 4i
Dissecting needle	TGK	Cat# 454-50-75-01
Surgical scissors	Natsume Seisakusho Co.,Ltd.	Cat# B-12
Benchtop centrifuge	Bio Medical Science	Cat# BSR-Mini6000KS
Silicon tips for bulb assembly	Drummond	Cat# 1-000-9003
60-mm dish	Falcon	Cat# 35-1007
60-mm dish for tissue culture	IWAKI	Cat# 3010-060
35-mm dish	Falcon	Cat# 35-1008
Thermo plate	Tokai Hit	Cat# Tpi-W
Inverted microscope	Olympus	IX73-SLICSI
Micromanipulators	NARISHIGE	IM-11-2
BOROSILICATE GLASS	SutterInstrument	Cat# B100-75-10
Micro loader	Eppendorf	Cat# 5242-956-003
Femtojet 4i	Eppendorf	Cat# 5252000021
Femtotip	Eppendorf	Cat# 930000035
Glass capillary, EM MYSTAR Hematocrit Capillary Plain Type	AS ONE	Cat# 9100175