REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K4me1	Diagenode	C15410194; RRID:AB_2637078
H3K4me3	Diagenode	C15410003-50; RRID:AB_2616052
H3K9me3	Diagenode	C15410193; RRID:AB_2616044
H3K27ac	Diagenode	C15410196; RRID:AB_2637079
H3K27me3	Diagenode	C15410195; RRID:AB_2753161
H3K36me3	Diagenode	C15410192; RRID:AB_2744515
RUNX1	Abcam	ab23980; RRID:AB_2184205
Critical Commercial Assays
KAPA library preparation kit	Kapa Biosystems	KK8400
riboZero gold rRNA removal kit	Illumina	MRZG12324
Nextera DNA Library Prep Kit	Illumina	FC-121-1031
TruSeq SBS KIT v3 - HS (50 cycles)	Illumina	FC-401-3002
NextSeq 500/550 High Output v2 kit (75 cycles)	Illumina	FC-404-2005
NEBNext High-Fidelity 2 × PCR Master Mix	New England Biolabs	M0541
Second Strand Buffer	Life Technologies	10812-014
Superscript III Reverse Transcriptase	Life Technologies	18080-044
DNase I	QIAGEN	79254
Qubit RNA HS assay kit	Life Technologies	Q32852
Ribozero Gold Kit	Illumina	MRZG12324
Rneasy Mini Kit	QIAGEN	74106
Deposited Data
Raw data files for histone ChIP sequencing	This paper	EGAD00001002340, EGAD00001002418, EGAD00001002935
Raw data files for RUNX1 ChIP sequencing	This paper; Mendeley Data	GSE111821; 10.17632/99vfrzcbhm.1
Raw data files for RNA sequencing	This paper	EGAD00001002443, EGAD00001002465, EGAD00001002962, EGAD00001002968
Raw data files for DNaseI sequencing	This paper	EGAD00001002355
Raw data files for WGBS sequencing	This paper	EGAD00001002333, EGAD00001002419
Raw data files for ATAC sequencing	Corces et al., 2016	GSE74912
Software and Algorithms
ConsensusClusterPlus	Wilkerson and Hayes, 2010	http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html
pvclust	Suzuki and Shimodaira, 2006	http://stat.sys.i.kyoto-u.ac.jp/prog/pvclust/
BWA	Li and Durbin, 2009	http://bio-bwa.sourceforge.net/
Picard	N/A	http://broadinstitute.github.io/picard/
PhantomPeakQualTools	N/A	https://code.google.com/archive/p/phantompeakqualtools/
MACS2	Zhang et al., 2008	https://github.com/taoliu/MACS
deepTools	Ramírez et al., 2016	https://github.com/deeptools/deepTools
ChromHMM	Ernst and Kellis, 2012	http://compbio.mit.edu/ChromHMM/
ChromDiff	N/A	http://compbio.mit.edu/ChromDiff/
ROSE	Whyte et al., 2013	http://younglab.wi.mit.edu/super_enhancer_code.html
BEDTools	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
STAR	Dobin et al., 2013	https://github.com/alexdobin/STAR
STAR-Fusion	Haas et al., 2017	https://github.com/STAR-Fusion
DESeq2	Love et al., 2014	http://bioconductor.org/packages/release/bioc/html/DESeq2.html
Cufflinks	Trapnell et al., 2010	http://cole-trapnell-lab.github.io/cufflinks/
MISO	Katz et al., 2010	https://miso.readthedocs.io/en/fastmiso/
F-Seq	Boyle et al., 2008	https://github.com/aboyle/F-seq
GEM	Marco-Sola et al., 2012	http://dat.cnag.cat/wiki/The_GEM_library
HOMER	Heinz et al., 2010	http://homer.ucsd.edu/homer/motif/
PIQ	Sherwood et al., 2014	https://bitbucket.org/thashim/piq-single
Cytoscape	Shannon et al., 2003	https://cytoscape.org/
bwtool	Pohl and Beato, 2014	https://github.com/CRG-Barcelona/bwtool
CIBERSORT	Newman et al., 2015	https://cibersort.stanford.edu/
IGV	Robinson et al., 2011	http://software.broadinstitute.org/software/igv/
Other
EpiFactors database	Medvedeva et al., 2015	http://epifactors.autosome.ru/