REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
B220-biotin	Biolegend	Cat#:103204; RRID: AB_312989
CD3e-biotin	Biolegend	Cat#:100244; RRID: AB_2563947
CD4-biotin	Biolegend	Cat#:100508; RRID: AB_312711
CD8a-biotin	Biolegend	Cat#:100704; RRID: AB_312743
CD19-biotin	Biolegend	Cat#:115504; RRID: AB_313639
CD11b-biotin	Biolegend	Cat#:101204; RRID: AB_312787
Gr1-biotin	Biolegend	Cat#:108404; RRID: AB_313369
Ter119-biotin	Biolegend	Cat#:116204; RRID: AB_313705
CD11c-biotin	Biolegend	Cat#:117304; RRID: AB_313773
NK1.1-biotin	Biolegend	Cat#:108704; RRID: AB_313391
Streptavidin-Pacific Orange	Invitrogen	Cat#:S32365
cKit-APC-Cy7	Biolegend	Cat#:105826; RRID: AB_1626278
Sca-PE-Cy7	Biolegend	Cat#:108114; RRID: AB_493596
Sca-PE-Cy5	Biolegend	Cat#:108110; RRID: AB_313347
CD48-APC	Biolegend	Cat#:103412; RRID: AB_57199
CD150-PE-Cy5	Biolegend	Cat#:115912; RRID: AB_493598
CD127-PE-Cy7	eBioscience	Cat#:25-1271-82; RRID: AB_469649
CD16/32-PE-Cy7	eBioscience	Cat#:25-0161-82; RRID: AB_469598
CD34-efluor660	eBioscience	Cat#:50-0341-82; RRID: AB_10596826
B220-APC	eBioscience	Cat#:17-0452-83; RRID: AB_469396
CD3-APC	Biolegend	Cat#:100236; RRID: AB_2561456
Mac1-APC	Biolegend	Cat#:101212
Gr1-APC	Biolegend	Cat#:108412; RRID: AB_313377
Ter119-APC	Biolegend	Cat#:116212; RRID: AB_313713
Chemicals, Peptides, and Recombinant Proteins
Polyinosinic:polycytidylic acid	Amersham	Cat#:24939-03-5
Isoflurane	Sigma-Aldrich	Cat#:792632-250MG
Lipopolysaccharide from E. coli 055:B5	Sigma-Aldrich	Cat#:L2880-10MG
Medium 199	ThermoFisher Scientific	Cat#:11043023
Fetal bovine serum	ThermoFisher Scientific	Cat#:10082139
RNase Out	ThermoFisher Scientific	Cat#:10777019
Calcein AM	ThermoFisher Scientific	Cat#:C3099
Propidium iodide	ThermoFisher Scientific	Cat#:P3566
NEBNext High-Fidelity 2X PCR Master Mix	New England Biolabs	Cat#:M0541L
Invitrogen SYBR Green I Dye	Invitrogen	Cat#:S7563
4OH-tamoxifen	Sigma	Cat#:T-5648
Progesterone	Sigma	Cat#:P-3972
Critical Commercial Assays
Smart-seq2 protocol	Picelli et al., 2013	N/A
Nextera XT	Illumina	Cat#:FC-131-1024
NuGen’s Ovation® Ultralow Methyl-Seq Library Systems	NuGen	Cat#:0335
REAGENT or RESOURCE	SOURCE	IDENTIFIER
QIAGEN Epitect Bisulfite kit	QIAGEN	Cat#:59104
Illumina Nextera DNA Preparation Kit	Illumina	Cat#:FC-121-1030
QIAGEN MinElute PCR purification Kit	QIAGEN	Cat#:28004
Deposited Data
HUe RNA-Seq data	GEO datasets http://www.ncbi.nlm.nih.gov/gds	GEO: GSE60101
129P2 WGBS data	GEO datasets http://www.ncbi.nlm.nih.gov/gds	GEO: GSE56986
BALBcJ WGBS data	GEO datasets http://www.ncbi.nlm.nih.gov/gds	GEO: GSE60485
129P2 sequence structure annotation files	http://www.sanger.ac.uk/science/programmes/mouse-and-zebrafish-genetics	129P2
BALBcJ sequence structure annotation files	http://www.sanger.ac.uk/science/programmes/mouse-and-zebrafish-genetics	BALBcJ
Referenced RNA-Seq data of hematopoietic subtypes	Lara-Astiaso et al., 2014	N/A
Experimental Models: Organisms/Strains
HUe mouse	This paper	N/A
C57BL6/J	Jackson Laboratories	000664
Mx1-Cre	Jackson Laboratories	003556
Prx1-CreER	This paper	N/A
Col(II)-CreER	Jackson Laboratories	006774
Recombinant DNA
HUe fluorescent cassette	Livet et al., 2007	#6 - CMV-Brainbow-2.1 “R” [GYRC]
pCAG promoter	www.addgene.org	Plasmid #13777
LoxP-STOP-LoxP-TOPO sequence	www.addgene.org	Plasmid #11584
LoxSL: ATAACTTCGTATA GTTCAACT TATACGAAGTTAT	This paper	N/A
Sequence-Based Reagents
Custom primers used for ATAC-Seq	This paper	Table S2
Software and Algorithms
FlowJo software	TreeStar Inc.	N/A
PAGODA package V1.99.3	Fan et al., 2016	http://pklab.med.harvard.edu/scde
MASS R package	N/A	https://cran.r-project.org/
MClust R package	N/A	https://cran.r-project.org/
BSMap 2.7	N/A	N/A
BIC-seq2	Xi et al., 2016	http://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/BICseq2.html
bowtie2	Johns Hopkins University	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
tophat2	Johns Hopkins University	https://ccb.jhu.edu/software/tophat/index.shtml
DESeq	Anders and Huber, 2010	https://www.bioconductor.org/
Homer package	Heinz et al., 2010	http://homer.salk.edu/homer/
SPP package 1.13	Kharchenko et al., 2008	http://compbio.med.harvard.edu/Supplements/ChIP-seq/
REAGENT or RESOURCE	SOURCE	IDENTIFIER
Other
BD FACSAria II Cell Sorter	BD Biosciences	N/A
Cesium 137 irradiator	N/A	N/A
Illumina Nexseq 500 instrument	Illumina	N/A