REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Tet2	Abcam	ab124297
Anti-Tet1	Genetex	GTX125888
Anti-Flag (for Western Blot)	Sigma	F1804
Anti-Flag (for ChIP)	CST	2368
Anti-Sin3a	Abcam	ab3479
Anti-H3K27ac	Abcam	ab4729
Rabbit IgG isotype control DA1E	CST	3900
Guinea pig anti-rabbit	Antibodies Online	ABIN101961
Anti-beta-actin	Abcam	AC-15
Anti-Vinculin	Proteintech	66305
Anti-5hmC	Active Motif	39069
Goat Anti-Rabbit IgG-HRP	Millipore	401393
Goat Anti-Mouse IgG-HRP	Millipore	401253
Alexa Flour 594 anti-rabbit	Life Technologies	A21207
Critical commercial assays
Omega E.Z.N.A. Total RNA kit	Omega	R6834-02
Quick-DNA miniprep kit	Zymo	D3024
Superscript III first strand	Invitrogen	18080-400
XtremeGene 9 DNA transfection reagent	Roche	06365787001
EpiQuik hMeDIP kit	Epigentek	P-1038-24
Deposited data
RNA-seq	This paper	GEO:GSE213398
CUT&Tag	This paper	GEO:GSE213398
WGBS	This paper	GEO:GSE213398
Experimental models: Cell lines
Tet2–/– mouse ESC	This paper	N.A.
Tet2m/m mouse ESC	This paper	N.A.
Tet2+/+;flag/flag mouse ESC	This paper	N.A.
Tet2m/m;flag/flag mouse ESC	This paper	N.A.
Oligonucleotides
RT-qPCR primers, see Table S2	This paper	N.A.
Genotyping primers, see Table S2	This paper	N.A.
gRNA oligos for gene targeting, see Table S2	This paper	N.A.
Recombinant DNA
Topo pcr2.1 Tet2 mutant donor vector	This paper	N.A.
pX330-Tet2-gRNA	This paper	N.A.
Software and algorithms
Trim galore v0.6.5	Babraham Institute	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
STAR v2.7.3a	N.A.	https://github.com/alexdobin/STAR
DESeq2 v1.20.0	N.A.	http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
DAVID 6.8	N.A.	https://david.ncifcrf.gov
Bismark v0.22.3	N.A.	https://github.com/FelixKrueger/Bismark
Methpipe v3.4.3	N.A.	http://smithlabresearch.org/software/methpipe/
HOMER v4.7	UCSD	http://homer.ucsd.edu/homer/motif/
ChIPseeker v1.30.3	Github	https://guangchuangyu.github.io/software/ChIPseeker/
Bedtools v2.30.0	N.A.	https://bedtools.readthedocs.io/en/latest/
deepTools v3.5.1	N.A.	https://deeptools.readthedocs.io/en/develop/index.html
Bowtie2 v2.4.5	John Hopkins University	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Integrative Genomics Viewer v2.12.3	Broad Institute	http://software.broadinstitute.org/software/igv/
MACS v2.2.7.1	Github	https://github.com/macs3-project/MACS
GraphPad Prism 9 v9.3.1	GraphPad	https://www.graphpad.com/
ImageJ v1.53	N.A.	https://imagej.nih.gov/ij/