REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rat anti-Mouse CD31-BV605 (clone 390)	BioLegend	Cat# 102427; RRID:AB_2563982
Rat anti-Mouse CD117-BV421 (c-Kit) (clone 2B8)	BD Biosciences	Cat#562609; RRID:AB_11154585
Armenian hamster anti-Mouse CD27-APC (clone LG.7F9)	eBioscience/Thermo Fisher Scientific	Cat# 17-0271-82; RRID: AB_469370
Rat anti-Mouse CD34-biotin (clone RAM34)	eBioscience/Thermo Fisher Scientific	Cat# 13-0341-82; RRID: AB_466425
Rabbit anti-GFP	MBL International	Cat# 598; RRID: AB_591819
Armenian hamster anti-Mouse CD27 (clone LG.7F9)	eBioscience/Thermo Fisher Scientific	Cat# 14-0271-82; RRID: AB_467183
Streptavidin-Alexa Fluor 555	Invitrogen/Thermo Fisher Scientific	Cat# s21381; RRID: AB_2307336
Goat anti-Rabbit IgG (H+L)-Alexa Fluor 488	Invitrogen/Thermo Fisher Scientific	Cat# A-11008; RRID: AB_143165
Goat anti-Armenian hamster IgG-Alexa Fluor 647 (clone Poly4055)	BioLegend	Cat# 405510, RRID:AB_2566695
APC anti-Mouse CD45.1 (clone A20)	BD Biosciences	Cat#558701; RRID:AB_1645214
PE anti-Mouse CD45.2 (clone 104)	BD Biosciences	Cat#560695; RRID:AB_1727493
Chemicals, Peptides, and Recombinant Proteins
Collagenase Type I from Clostridium histolyticum	Sigma-Aldrich	Cat#C0130; Lot#02M1425V
Foetal Bovine Serum Standard Quality	Brunschwig Chemie BV	Cat#BS01500; Lot#212-223650
10% Triton X-100	Sigma-Aldrich	Cat#93443-100 ml
SUPERase-In RNase Inhibitor	Ambion	Cat#AM2694
dNTP mix	ThermoFisher	Cat#10319879
ERCC RNA Spike-In Mix	ThermoFisher	Cat#4456740
Superscript II Reverse Transcriptase	ThermoFisher	Cat#18064-014
Betaine	Sigma-Alrich	Cat#B0300
Magnesium chloride	ThermoFisher	Cat#AM9530G
KAPA HiFi Hotstart ReadyMix	KAPA Biosystems	Cat#KK2601
Agencourt AMPure XP beads	Beckman Coulter	Cat#A63881
EB solution	QIAGEN	Cat#19086
Critical Commercial Assays
High-sensitivity DNA chip	Agilent	Cat#5067-4626
Quant-iT Picogreen double stranded DNA assay kit	ThermoFisher	Cat#P7589
Nextera XT DNA sample preparation kit 96 samples	Illumina	Cat#FC-131-1096
Nextera XT 96-Index kit, 384 samples	Illumina	Cat#FC-131-1002
KAPA qPCR quantification kit	KAPA Biosystems	Cat# KK4824
Deposited Data
Single-cell RNaseq	This paper	Accession number: GSE143637
Experimental Models: Organisms/Strains
Mouse: Gata2Venus	Laboratory of Elaine Dzierzak; Kaimakis et al., 2016, Blood	N/A
Mouse: B6.Cg-Tg(Ly6a-EGFP)G5Dzk/J	The Jackson Laboratory	https://www.jax.org/strain/012643
Mouse: B6.Cg-Tg(Csf1r-EGFP)1Hume/J (also known as MacGreen)	The Jackson Laboratory	https://www.jax.org/strain/018549
Mouse: B6.SJL-PtprcaPepcb/BoyCrl (also known as Ly5.1)	Charles River	Strain code: 494 https://www.criver.com/products-services/find-model/ly51-mouse?region=3671
Mouse: C57BL/6JOlaHsd	Envigo	Order code: 057 https://www.envigo.com/products-services/research-models-services/models/research-models/mice/inbred/c57bl-6-inbred-mice/c57bl-6jolahsd/u.k.aspx
Oligonucleotides
TSO: AAGCAGTGGTATCAACG CAGAGTACATrGrG+G-3′	Picelli et al., 2014	N/A
Oligo-dT30VN: AAGCAGTGGTATCA ACGCAGAGTAC(T30)VN-3′	Picelli et al., 2014	N/A
ISPCR: AAGCAGTGGTATCAACG CAGAGT	Picelli et al., 2014	N/A
Software and Algorithms
Prism Version 7	GraphPad	http://www.graphpad.com/scientific-software/prism
BD Facs Diva version 8	BD Biosciences	http://www.bdbiosciences.com/en-us
FlowJo Version 10.1r5	Tree Star, Inc	https://www.flowjo.com/solutions/flowjo/downloads/previous-versions
GSNAP	Wu et al., 2016	http://research-pub.gene.com/gmap/
HTSeq	Anders et al., 2015	https://htseq.readthedocs.io/en/release_0.11.1/install.html
PCA	Becker et al., 1988	prcomp in R stats package
Selection of Highly Variable Genes	Brennecke et al., 2013	https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.2645/MediaObjects/41592_2013_BFnmeth2645_MOESM313_ESM.pdf
ICGS	Olsson et al., 2016	https://altanalyze.readthedocs.io/en/latest/ICGS/
DESeq2	Love et al., 2014	http://bioconductor.org/packages/release/bioc/html/DESeq2.html
SPRING	Weinreb et al., 2018	https://github.com/AllonKleinLab/SPRING
hscScore	Hamey and Göttgens, 2019	https://github.com/fionahamey/hscScore
Other
Interactive website	This paper	https://gottgens-lab.stemcells.cam.ac.uk/DZIERZAK/
Single-cell RNaseq	Zhou et al., 2016	Accession number: GSE67120