REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-mouse: CCR6-PE	Biolegend	Cat# 129804; RRID: AB_1279137
Anti-mouse CD3-BV650	Biolegend	Cat# 100229; RRID: AB_11204249
Anti-mouse CD3-BV785	Biolegend	Cat# 100231; RRID: AB_11218805
Anti-mouse CD3-PE-Cy7	Biolegend	Cat# 152314; RRID: AB_2629847
Anti-mouse CD3-eFluor660	Invitrogen	Cat# 50-0032-82; RRID:AB_10598657
Anti-mouse CD31-BV480	BD Bioscience	Cat# 746260; RRID: AB_2743592
Anti-mouse CD4-APC-eFluor780	eBioscience	Cat# 47-0041-82; RRID: AB_11218896
Anti-mouse CD4-BV785	Biolegend	Cat# 100551; RRID: AB_11218992
Anti-mouse CD4-PE	eBioscience	Cat# 12-0042-82; RRID: AB_465510
Anti-mouse CD5-PE-Cy7	Biolegend	Cat# 100622; RRID: AB_2562773
Anti-mouse CD8- APC Cy7	BioLegend	Cat# 100714; RRID: AB_312753
Anti-mouse CD11b-APC-Cy7	Biolegend	Cat# 101226; RRID: AB_830642
Anti-mouse CD11c PE-CF594	BD Bioscience	Cat# 562454; RRID: AB_2737617
Anti-mouse CD19-BV421	Biolegend	Cat# 115537; RRID: AB_10895761
Anti-mouse CD19- BV785	Biolegend	Cat# 115543; RRID: AB_11218994
Anti-mouse CD19- PE-Cy7	Biolegend	Cat# 115520; RRID: AB_313655
Anti-mouse CD44- APC Cy7	Biolegend	Cat# 103028; RRID: AB_830785
Anti-mouse CD103 Biotinylate	BD Bioscience	Cat# 557493; RRID: AB_396730
Anti-mouse CD62L BV510	Biolegend	Cat# 104441; RRID: AB_2561537
Anti-mouse CD45-BUV395	BD Bioscience	Cat# 564279; RRID: AB_2651134
Anti-mouse CD90 – BV605	Biolegend	Cat# 140317; RRID: AB_11203724
Anti-mouse CD127-FITC	eBioscience	Cat# 11-1271-82; RRID: AB_465195
Anti-mouse CX3CR1-FITC	Biolegend	Cat# 149020; RRID: AB_2565703
Fixable Viability dye – efluor450	eBioscience	Cat# 65-0863-14
Fixable Viability dye – efluor506	eBioscience	Cat# 65-0866-14
Anti-mouse FceRIα-PE-Cy7	Biolegend	Cat# 134318; RRID: AB_10640122
Anti-mouse Foxp3-AF700	eBioscience	Cat# 56-5773-82; RRID: AB_1210557
Anti-mouse F4/80-APC	Biolegend	Cat# 123116; RRID: AB_893481
Anti-mouse Gata3-AF647	BD Bioscience	Cat# 560068; RRID: AB_1645316
Anti-GFP AF488	Thermo Fisher Scientific	Cat# A-213111; RRID: AB_221477
Anti-mouse I-A/I-E-AF700	Biolegend	Cat# 107622; RRID: AB_493727
Anti-mouse I-A/I-E-BV650	Biolegend	Cat# 107641; RRID: AB_2565975
Anti-mouse Il-22-APC	eBioscience	Cat# 17-7222-82; RRID: AB_10597583
Anti-mouse KI-67 Percp-Cy55	BD Bioscience	Cat# 561284; RRID: AB_10611574
Anti-mouse Ly6C-BV421	Biolegend	Cat# 128032; RRID: AB_2562178
Anti-mouse Ly6G-PE-Cy7	Biolegend	Cat# 127618; RRID: AB_1877261
Anti-mouse NK1.1-APC	Biolegend	Cat# 108720; RRID: AB_2132713
Anti-mouse Neuropilin1-PE	Biolegend	Cat# 145204; RRID: AB_2561928
Anti-mouse Nkp46-PercP-Cy5.5	Biolegend	Cat# 137610; RRID: AB_10641137
Anti-mouse RORγt-PE	eBioscience	Cat# 12-6981-82; RRID: AB_10807092
Anti-mouse Siglec F-PE	Biolegend	Cat# 155506; RRID: AB_2750235
Streptavidin-PE-Cy7	Bioscience	Cat# 557598; RRID: AB_10049577
Anti-mouse Tbet-PECy7	eBioscience	Cat# 25-5825-82; RRID: AB_11042699
Anti-mouse Thy 1.1	eBioscience	Cat# 11-0902-82; RRID: AB_465154
Anti-mouse Thy 1.2	Biolegend	Cat# 140318; RRID: AB_2650924
Rat IgG1 isotype control PE	Thermo Fisher Scientific	Cat# 12-4301-81; RRID:AB_470046
Monoclonal anti-mouse Ki-67 (Tec3 Ab)	Dako, Glostrup Denkmark	Cat# M7249
InVivoMAb rat anti-mouse IgG2b	BioXcell	Cat# BE0090; RRID: AB_1107780
InVivoMAb anti-mouse CD4	BioXcell	Cat# BE0003-1; RRID:AB_1107636
InVivoMAb anti-mouse CD90.2 (30H12)	BioXcell	Cat# BE0066; RRID: AB_1107682
Chemicals, peptides, and recombinant proteins
Formaldehydlösung 4% neutral	SAV Liquid Production GmbH	Cat# FN-5000-4-1
Percoll	Sigma-Aldrich	Cat# P1644-1L
Dulbeccos PBS (w/o calcium and magnesium) (DPBS)	Gibco	Cat# 4190-094
Dulbeccos PBS (w calcium and magnesium) (PBS)	Gibco	Cat# D8662
High Capacity cDNA Reverse Transcription Kit	Thermo Fisher Scientific	Cat# 4368813
DNAse	Sigma-Aldrich	Cat# DN25-5g
Collagenase D	Sigma-Aldrich	Cat# 11088882001
Dispase	Corning	Cat# 354235
DNAse I	Roche	Cat# 05952077103
Collagenase IV	Worthington	Cat# LS0004186
Collagenase IA	Sigma	Cat# C9891
Collagenase VIII	Sigma	Cat# C2139
Trizol	Thermo Fisher Scientific	Cat# 15596026
HEPES	Gibco	Cat# 15630-056
BSA	Sigma-Aldrich	Cat# A7030-100G
Dulbecco’s Modified Eagle Medium (DMEM)	Gibco	Cat# 41965062
Iscove’s Modified Dulbecco’s Medium (IMDM)	Gibco	Cat# 21980032
HEPES (1 M)	Gibco	Cat# 15630080
Fetal bovine serum	Pan-Biotech	Cat# P30-3602
Chloroform	Sigma Aldrich	Cat# 288306-100ML
70 kD Fluorescein isothiovyanate (FITC)-dextran	Sigma	Cat# 46945-100MG
MacConkey II agar	BD BBL	Cat# 212306
Schaedler Agar	BD BBL	Cat# 212189
Sheep blood defibrinated	Oxoid	Cat# SR0051E
Kanamycin sulfate	Sigma-Aldrich	Cat# 60615
Vitamin-K3 (Menadion)	Sigma-Aldrich	Cat# M5625
Columbia blood agar base	Oxoid	Cat# CM331
GC agar base	BD Difco	Cat# 228950
Hemoglobin	Oxoid	Cat# LP0053
Difco supplement VX	BD Difco	Cat# 233541
Brain heart infusion	Oxoid	Cat# CM1135
Hemin	Sigma-Aldrich	Cat# 51280-1G
Vitamin-K1	Sigma-Aldrich	Cat# 95271-1G
Bacto Tryptone	BD	Cat# 211699
Bacto Yeast Extract	Gibco	Cat# 212750
Sodium chloride	Sigma-Aldrich	Cat# S9625-5KG
Agar	Sigma-Aldrich	Cat# 05039-500G
Sakura Finetek™ Tissue-Tek™ O.C.T. Compound	Sakura	Cat# 12351753
SuperFrost® Plus	VWR	Cat# 631-9483
Triton X-100	Sigma-Aldrich	Cat# X100-100ML
Saccharose	Sigma-Aldrich	Cat# S9378-500G
Fluoromount-G	Invitrogen	Cat# 00-4958-02
Mouse Serum	Life Science	Cat# S-012L
EDTA	Thermo Fisher Scientific	Cat# AM9912
Lysozyme	Sigma	Cat# 62970-5G-F
Streptomycin	Sigma-Aldrich	Cat# S6501
Gelatin from cold water fish skin (GCWFS)	Sigma	Cat# G7041
DAPI	Carl Roth	Cat# 6843.1
Normal Mouse Serum	Invitrogen	Cat# 10410
Critical commercial assays
Blocking Kit VE Avidin/Biotin	Vector laboratories	Cat# SP-2001
FoxP3 staining kit	Thermo Fisher Scientific	Cat# 00-5521-00
Cytofix/cytoperm Buffer	BD Bioscience	Cat# 554722
miRNeasy Micro Kit	Qiagen	Cat# 217084
High-Capacity cDNA Reverse Transcription Kit	Applied Biosystems	Cat# 4368813
SYBR™ Green PCR Master Mix	Applied Biosystems	Cat# 4334973
Taqman™ Universal Master Mix	Thermo Fisher	Cat# 4440039
QIAamp DNA stool kit	Qiagen	Cat# 51604
Qubit dsDNS BR Assay-Kit	Thermo Fisher Scientific	Cat# Q32853
Qubit dsDNS HS Assay-Kit	Thermo Fisher Scientific	Cat# Q32854
Deposited data
Bulk RNA-seq (of liver pre- and post-partial hepatectomy)	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158174	code: cdunemgsdnixjyb
Experimental models: Organisms/strains
C57BL/6J (wild-type)	Envigo	N/A
B6.PL-Thy1a/CyJ		RRID:IMSR_JAX:000406
B6.FVB-Tg(Rorc-cre)tm1Litt/J	Eberl et al.16	N/A
B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J	Srinivas et al.67	RRID:IMSR_JAX:006148
B6.129P2-Rorctm1Litt/J	Sun et al.68	RRID:IMSR_JAX:007571
B6.129S7-Rag1tm1Mom/J	Mombaerts et al.69	RRID:IMSR_JAX:002216
Rag2−/−	Hao et al.70	N/A
IGIF−/−(IL-18−/−)		N/A
B6.Il22−/−	Kreymborg et al.71	N/A
Pycard−/−(Asc−/−)	Drexler et al.72	N/A
Oligonucleotides
See Table S2 for Oligonucleotides and RNA sequences		N/A
Software and algorithms
FlowJo10.4	Tree Star	https://www.flowjo.com RRID: SCR_008520
R studio	R foundation	https://www.r-project.org RRID: SCR_000432
Prism 8	GraphPad software, Inc.	www.graphpad.com RRID: SCR_002798
ImageJ 1.8.0	Image J Software	https://imagej.nih.gov/ij/
Leica Application Suite X	Leica Microsystems	https://www.leica-microsystems.com RRID: SCR_013679
Qiime	QIIME development team	https://qiime2.org
Imaris	Oxford Instruments	https://imaris.oxinst.com