REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Zombie Aqua™ Fixable Viability Kit	BioLegend	Cat# 423101
Mouse anti-rat CD45 BV786; Clone: OX-1	BD Biosciences	Cat#740914; RRID: AB_2740556
Mouse anti-rat CD11b V450; Clone: WT.5	BD Biosciences	Cat# 562108; RRID: AB_10898164
Mouse anti-rat CD3 PE; Clone: 1F4	BD Biosciences	Cat# 550353; RRID: AB_393632
Mouse anti-rat CD3 BV510; Clone: 1F4	BD Biosciences	Cat# 624289
Mouse anti-rat CD68 AF700; Clone: ED1	Novus Biologicals	Cat# NB600-985AF700
Mouse anti-rat CD11a PE; Clone: ED1	BD Biosciences	Cat# 550972; RRID: AB_393985
Recombinant anti-mouse/rat TNFα; Clone: EPR21753-109	AbCam	Cat# ab283321
Mouse anti-rat CD32; Clone: D34-485	BD Biosciences	Cat# 562189; RRID: AB_11153308
Recombinant anti-rat CD68; Clone: REA237	Miltenyi Biotec	Cat# 130-102-723; RRID: AB_2659012
LEGENDplex™ Rat Inflammation Panel Detection Antibodies V02	Biolegend	Cat# 740266; RRID: SCR_001134
Rabbit anti-CD3; Clone: 2GV6	Roche Diagnositics	Cat# 05278422001; RRID: AB_2335978
Mouse anti-rat CD8α; Clone: OX-8	Bio-Rad	Cat# MCA48G; RRID: AB_321476
Mouse anti-Bovine/Dog/Human/Mouse/Rat Hmox1; Clone: HO-1-1	Thermo Fisher Scientific	Cat# MA1-112; RRID: AB_2536823
Rabbit anti-Mouse/Rat CD68; Clone: Polyclonal	AbCam	Cat# ab125212; RRID: AB_10975465
Mouse-anti rat CD163; Clone: ED2	BioRad	Cat# MCA342GA
Chemicals, peptides, and recombinant proteins
Heparin	LEO	Cat# 006174-0
20G cannula	Braun	Cat# 4252535-02
Hank’s Balanced Salt Solution	Gibco	Cat# 14170161
EGTA	Bioshop	Cat# EGT101
DMEM with HEPES	Gibco	Cat#21063045
Fetal bovine serum	Cytiva	Cat# SH3039603
Penicillin-streptomycin	Sigma-Aldrich	Cat# P4333
Lipopolysaccharide; Lot# 028M4094V	Sigma-Aldrich	Cat# L2880-250MG
Golgiplug (Brefeldin)	Biolegend	Cat# 555029
Golgistop (Monensin)	Biolegend	Cat# 554724
Collagenase	Sigma-Aldrich	Cat# C5138
CaCl2	Sigma-Aldrich	Cat# 21115
Tris-HCl pH 7.5	Thermo Fisher Scientific	Cat# 15567027
NaCl	Sigma-Aldrich	Cat# 59222C
MgCl2	Sigma-Aldrich	Cat# M1028
Ultrapure RNase/DNase free distilled water	Thermo Fisher Scientific	Cat# 10977023
SYBR Green	Thermo Fisher Scientific	Cat#S7564
CHAPS hydrate	Sigma-Aldrich	Cat# C3203
Bovine Serum Albumin	New England BioLabs	Cat# B9000S
HEPES	Gibco	Cat# 15630080
Critical commercial assays
Transcription Factor and Staining Buffer Set	eBioscience	Cat# 00-5523-00
Chromium Single Cell Reagents 3′ Library & Gel Bead Kit v2, 16 rxns	10x Genomics	Cat# PN-120237
Cytofix/Cytoperm	BD Biosciences	Cat# 20554714
Single Cell Reagents 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns	10x Genomics	Cat# PN-1000075
Chromium Next GeM Chip A	10x Genomics	Cat# PN-120236
EasySep™ FITC Positive Selection Kit II	Stem Cell Technologies	Cat# 17682
Visium Spatial Tissue Optimization Slide Kit v1	10x Genomics	Cat# PN-1000191
Visium Spatial Tissue Optimization Reagent Kit v1	10x Genomics	Cat# PN-1000192
Library Construction Kit	10x Genomics	Ca# PN-1000190
Visium Spatial Gene Expression Slide Kit	10x Genomics	Cat# PN-1000185
Dual Index Kit TT Set A	10x Genomics	Cat# PN-1000215
Chromium Next GEM Chip G B	10x Genomics	Cat# PN-1000073
Deposited data
Raw and analyzed data	This Paper	GEO: GSE220075
Interactive sc/snRNA-seq and spatial maps	This Paper	https://rat-liver-atlas.cells.ucsc.edu
Experimental models: Organisms/strains
Rat LEW/SsNHsd	Envigo	Cat#017
Rat DA/OlaHsd	Envigo	Cat#092
Rat Wistar	Envigo	Cat#012
Software and algorithms
GraphPad Prism 9	GraphPad Software	https://www.graphpad.com/
FlowJo 10	Treestar	https://www.flowjo.com/solutions/flowjo
Qognit™ LegendPlex™ Software	Biolegend	https://legendplex.qognit.com/
Qupath 0.2.3	Qupath	https://qupath.github.io/
10x Genomics CellRanger v3.1.0	Zheng et al.102	https://www.10xgenomics.com/
10x Genomics SpaceRanger v1.1.0	N/A	https://www.10xgenomics.com/
R v4.0.3	N/A	https://www.R-project.org/
Seurat v4.0.2	Hao et al.103	https://github.com/cran/Seurat
Harmony v1.0	Korsunsky et al.40	https://github.com/immunogenomics/harmony
scDblFinder v1.10.0	Germain et al.104	https://github.com/plger/scDblFinder
ggplot2	Wickham.105	https://github.com/tidyverse/ggplot2
scClustViz	Innes and Bader.106	https://github.com/BaderLab/scClustViz
NEBULA v1.3.0	He et al.82	https://github.com/lhe17/nebula
randomForest v4.6.14	Breiman.107	https://github.com/cran/randomForest/
caTools v1.18.2	N/A	https://CRAN.R-project.org/package=caTools
UCell v1.0.0	Andreatta and Carmona.108	https://github.com/carmonalab/UCell
Gene Set Enrichment Analysis (GSEA)	Subramanian et al.109	software. broadinstitute.org/GSEA
gProfile	Reimand et al.110	https://biit.cs.ut.ee/gprofiler/gost
Cytoscape v3.8.2	Shannon et al.111	https://cytoscape.org/
EnrichmentMap v3.3.2	Merico et al.112,113	https://apps.cytoscape.org/apps/enrichmentmap
AutoAnnotate v1.3.4	Kucera et al.112,113	https://apps.cytoscape.org/apps/autoannotate
biomaRt v2.46.2	Durinck et al.114	https://github.com/grimbough/biomaRt
Analysis code	This Paper	https://github.com/BaderLab/HealthyRatLiverMap
Other
LSR Fortessa	BD Biosciences	N/A
NovaSeq 6000	Illumina	N/A
HiSeq 2500	Illumina	N/A
EasyEights™ EasySep™ Magnet	Stem Cell	Cat# 18103
Epredia™ CryoStar™ NX70 Cryostat	Fisher Scientific	Cat#14-071-407
Leica Aperio AT2 whole slide scanner	Leica Microsystems	N/A
Rat/Mouse Chow	Harland-Teklad	Cat#LM-485 7912.15