REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-H3K4me3	MBL	Cat#MABI-0304 (lot:14004); RRID: AB_11123891
Anti-H3K9me2	MBL	Cat#MABI-0317 (lot:16001)
Anti-H3K9me3	MBL	Cat#MABI-0318 (lot:16001)
Anti-H3K27me3	MBL	Cat#MABI-0323 (lot:15007); RRID: AB_11123929
Anti-ATF7	B.C. supplied	2F10
Chemicals, peptides, and recombinant proteins
Trizol	Thermo Fisher	Cat#15596018
Collagenase	Sigma	Cat#C6138
Trypsin	Wako	Cat#208-17251
DNase I	Takara	Cat#2270A
BSA	Sigma	Cat#A7906
Percoll	GE Healthcare	Cat#17-0891-02
protein A-sepharose beads	GE Healthcare	Cat#17-0780-01
anti-mouse IgG-conjugated magnetic beads	Thermo Fisher	Cat#11201D
RNase A	Thermo Fisher	Cat#EN0531
proteinase K	Millipore	Cat#1.24568
phenol:chloroform:isoamyl alcohol	Wako	Cat#311-90151
AMPure XP beads	Beckman Coulter	Cat#A63881
Critical commercial assays
QuantiFast SYBR Green PCR Kit	Qiagen	Cat# 204056
NEBNext Ultra II DNA Library Prep Kit	NEB	Cat#E7645
Illumina NextSeq500 with High Output Kit v2	Illumina	Cat#FC-404-2005
NEBNext Small RNA Library Prep Kit	NEB	Cat#E7300
Deposited data
ChIP-seq data	This paper	DDBJ: DRA010655 (https://ddbj.nig.ac.jp/DRASearch/submission?acc=DRA010655)
Small RNA-seq data	This paper	DDBJ: DRA010655 (https://ddbj.nig.ac.jp/DRASearch/submission?acc=DRA010655)
refGene	UCSC Table Browser	https://genome.ucsc.edu/cgi-bin/hgTables
Mouse tRNA sequence	GtRNAdb	http://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc10/mm10-tRNAs.fa
Mouse miRNA sequence	miRBbase	http://www.mirbase.org/ (Release 22)
Experimental models: organisms/strains
Mouse: C57BL6/wild-type	Jackson Laboratory	N/A
Oligonucleotides
Primers for qChIP assay	This paper	Table S6
Software and algorithms
CLC Genomics Workbench	Qiagen	10.1.1
BED tool	Quinlan and Hall (2010)	2.27.0
MACS2	Feng et al. (2012)	2.1.1
deepTools2	Ramírez et al. (2016)	3.1.2.0.1
PANTHER classification system	Mi et al. (2013)	14.0
SPOTS1.0	Shi et al. (2018)	1.0.5
GSEA	Subramanian et al.(2005)	4.0.3
mirPath v.3	Vlachos et al. (2015)	http://snf-515788.vm.okeanos.grnet.gr/