REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3	10x Genomics	PN-1000075
Chromium Chip B Single Cell Kit	10x Genomics	PN-1000073
Chromium i7 Multiplex Kit	10x Genomics	PN-120262
Chromium Single Cell ATAC Library & Gel Bead Kit	10x Genomics	PN-1000110
Chromium Chip E Single Cell ATAC Kit	10x Genomics	PN-1000155
Chromium i7 Multiplex Kit N, Set A	10x Genomics	PN-1000084
Visium Spatial Gene Expression Slide & Reagent Kit	10x Genomics	PN-1000187
Visium Accessory Kit	10x Genomics	PN-1000194
Dual index Kit TT set A	10x Genomics	PN-1000215
Deposited data
Raw and processed scRNA-seq data	This paper	GSE190225
Raw and processed scATAC-seq data	This paper	GSE190225
Raw and processed ST data	This paper; Mendeley Data	GSE190225; https://doi.org/10.17632/2yr6y6wnc5.1
Cohen et al.’s raw and processed scRNA-seq data	Cohen et al., 2018	GSE119228
Experimental models: Organisms/strains
C57BL/6J, mus musculus	The Jackson Laboratory	IMSR_JAX:000664
Software and algorithms
Cell Ranger	10x Genomics	Version 3.1.0
Cell Ranger ATAC	10x Genomics	Version 1.1.0
Space Ranger	10x Genomics	Version 1.2.2
Seurat	https://satijalab.org/seurat/index.html	Version 4.0.1
RCTD	https://github.com/dmcable/RCTD	Version 1.2.0
Signac	https://satijalab.org/signac/index.html	Version 1.1.1
SCENIC	https://github.com/aertslab/SCENIC	Version 1.2.4
AUCell	https://github.com/aertslab/AUCell	Version 1.12.0
QuPath	https://qupath.github.io	Version 0.2.3
limma	https://bioconductor.org/packages/release/bioc/html/limma.html	Version 3.46.0
PANTHER Classification System	http://www.pantherdb.org	Version 16.0
MAST	https://www.bioconductor.org/packages/release/bioc/html/MAST.html	Version 1.16.0
clusterProfiler	https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html	Version 3.18.1
CellChat	https://github.com/sqjin/CellChat	Version 1.1.0
Other
Eclipse 90i Motorized Upright Microscope	Nikon	Eclipse 90i