REAGENT OR RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD45 30-F11 1 in 400 Mouse	eBioscience	45-0451-82
TER119 Ter-119 1 in 400 Mouse	eBioscience	12-5921-82
CD31 390 1 in 400 Mouse	eBioscience	25-0311-82
EasySep Human CD34 Positive Selection kit	StemCell Technologies	17856
EasySep Human CD45 Positive Selection kit	StemCell Technologies	100-0105
EasySep Mouse CD45 Positive Selection kit	StemCell Technologies	18945
InVivoMAb anti-human CD3	Euromedex/ Bioxcell	BE0001-2
Bacterial and virus strains
sLP–mCherry pRRL lentiviral backbone	Ombrato et al., 2019, 2021	N/A
Biological Samples
See Table 1	N/A	N/A
Chemicals, peptides, and recombinant proteins
DNase I	Sigma-Aldrich	D4527
Collagenase	Sigma-Aldrich	C0130
Dispase II	Sigma-Aldrich	D4693
Heparin	Sigma-Aldrich	H3149
Critical commercial assays
SomaScan® Platform	Somalogic	https://lifesciences.somalogic.com/technology
Ovation® RNA-Seq System V2 kit (part No. 7102	Nugen	M01206 v9
RNeasy Mini kit	QIAGEN	74106
Deposited data
RNA-sequencing data	Geo Bank	GSE148626
Secretome data	N/A	Table S5
Experimental models: Cell lines
HL60	ATCC	Cell Service, The Francis Crick Institute
ML1	ATCC	Cell Service, The Francis Crick Institute
Experimental models: Organisms/strains
NOD-SCID IL2Rgnull (NSG)	Jackson Laboratory	005557
NSG-NESTIN-EGFP	The original strain is a kind gift from Dr G. Enikolopov. Backcrossed to NSG background at the BRF, The Francis Crick Institute (generation 8)	N/A
NSG-NG2-DSRED	Original strain from Jackson Laboratory (008241). Backcrossed to NSG background at the BRF, The Francis Crick Institute (generation 8)	N/A
NSG-COL2.3-CFP	The original strain is a kind gift from Dr DW Rowe. Backcrossed to NSG background at the BRF, The Francis Crick Institute (generation 8)	N/A
NSG-OSX-CRE-GFP	Original strain from Jackson Laboratory (006361). Backcrossed to NSG background at the BRF, The Francis Crick Institute (generation 8)	N/A
Software and algorithms
FACSDiva	BD	N/A
FlowJo	FlowJo	Version 9.9
CASAVA BCL to FastQ	N/A	Version 2.16
RSEM package	N/A	Version 1.2.29
STAR alignment algorithm	N/A	Version 2.5.1b
DESeq2 package	N/A	Version 1.22.2
R programming environment	N/A	Version 3.2.3
Bioplotr package	N/A	N/A
prcomp function	N/A	N/A
plot3d function from the rgl package	N/A	N/A
Pheatmap package on R	N/A	N/A
“limma” package	N/A	N/A
Density-based algorithm	Rodriguez and Laio, 2014	N/A
Model-based Bayesian method	Adapted from Diana et al., 2019	N/A
Dynamic figure of ligand-receptor interaction	https://github.com/giovannidiana/integratedomics	https://giovannidiana.github.io/integratedomics/