KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-Biotin A0436 | Biolegend | RRID: AB_2801086; Cat#409008 |
| BDCA-2 FITC (AC144) | Miltenyi | RRID: AB_244167; Cat# 130-090-510 |
| CD103 A0145 | Biolegend | RRID: AB_2749996; Cat#350231 |
| CD103 AF700 (Ber-ACT8) | NOVUS | RRID: AB_11189940; Cat# NBP1-97564AF700 |
| CD107a PE (H4A3) | Biolegend | RRID: AB_1186062; Cat#328607 |
| CD117 APC-Fire750 (104D2) | Biolegend | RRID: AB_2632949; Cat#313240 |
| CD117 BUV395 (YB5.B8) | BD Biosciences | RRID: AB_2743211; Cat#745740 |
| CD117 BV650 (104D2) | Biolegend | RRID: AB_2721550; Cat#313222 |
| CD117 PE-Cy7 (104D2 | Biolegend | RRID: AB_893222; Cat#313212 |
| CD127 BV605 (A019D5) | Biolegend | RRID: AB_2562022; Cat#351334 |
| CD14 FITC (M5E2) | Biolegend | RRID: AB_314186; Cat#301804 |
| CD16 APC-H7 (B73.1) | BD Biosciences | RRID: AB_10643005; Cat#561306 |
| CD161 APC Cy7 (HP-3G10) | Biolegend | RRID: AB_2563967; Cat#339928 |
| CD19 FITC (HIB19) | Biolegend | RRID: AB_314236; Cat#302206 |
| CD1a FITC (HI149) | Biolegend | RRID: AB_314018; Cat#300104 |
| CD20 FITC (2H7) | Biolegend | RRID: AB_314252; Cat#302304 |
| CD200R APC (OX-108) | BioLegend | RRID: AB_2564351; Cat#329308 |
| CD200R Biotin (REA725) | Miltenyi | RRID: AB_2656117; Cat#130-111-289 |
| CD200R PE/Dazzle 594 (OX-108) | Biolegend | RRID: AB_2565526; Cat#329310 |
| CD200R1 BV421 (OX-108) | Biolegend | RRID: AB_2800856; Cat#329314 |
| CD200R1 PE (OX-108) | Biolegend | RRID: AB_2074200; Cat#329306 |
| CD3 FITC (UCHT1) | Biolegend | RRID: AB_314060; Cat#300406 |
| CD34 FITC (581) | Biolegend | RRID: AB_1731852; Cat#343504 |
| CD4 APC-Cy7 (RPA-T4) | Biolegend | RRID: AB_314086; Cat#300518 |
| CD44 Pe-Cy7 (BJ18) | Biolegend | RRID: AB_2716000; Cat#338815 |
| CD45 BUV395 (HI 30) | BD Biosciences | RRID: AB_2869519; Cat#563792 |
| CD45 BUV805 (HI30) | Biolegend | RRID: AB_2174123; Cat#304029 |
| CD45RA APC-Vio770 | Miltenyi | RRID: AB_2658317; Cat#130-108-717 |
| CD49a A0575 | Biolegend | RRID: AB_2783195; Cat#328315 |
| CD49a PerCP-e710 (TS2/7) | eBiosciences | RRID: AB_2573891; Cat#46-9490-42 |
| CD49e APC (NKI-SAM-1) | Biolegend | RRID: AB_2128193; Cat#328012 |
| CD5 PE/Dazzle 594 (UCHT2) | Biolegend | RRID: AB_2632673; Cat#300634 |
| CD52 A0033 | Biolegend | RRID: AB_2734292; Cat#316017 |
| CD52 APC (QA19A22) | Biolegend | RRID: AB_830793; Cat# 318906 |
| CD56 A0047 | Biolegend | RRID: AB_2749970; Cat#362557 |
| CD56 BUV563 (NCAM16.2) | BD Biosciences | RRID: AB_2744431; Cat#565704 |
| CD69 A0146 | Biolegend | RRID: AB_2749997; Cat#310947 |
| CD69 BV785 (FN50) | BD Biosciences | RRID: AB_2738441; Cat#563834 |
| CD9 APC Vio770 (REA1071) | Miltenyi | RRID: AB_2733145; Cat#130-118-871 |
| CD94 A0867 | Biolegend | RRID: AB_2814142; Cat#305521 |
| CD94 AF700 (DX22) | Novus | RRID: AB_962803; Cat#NB100-64104AF700 |
| CD94 BUV737 (HP-3D9) | BD Biosciences | RRID: AB_2873190; Cat#748787 |
| CD94 FITC (DX22) | Biolegend | RRID: AB_314534; Cat#305504 |
| ckit PE-Cy7 (104D2 | Biolegend | RRID: AB_893222; Cat#313212 |
| CRTH2 AF647 (BM16) | Biolegend | RRID: AB_10642025; Cat#350104 |
| CXCR3 BV605 (G025H7) | Biolegend | RRID: AB_2562200; Cat#353727 |
| CXCR4 BV421 (12G5) | Biolegend | RRID: AB_11146018; Cat#306518 |
| CXCR6 A0804 | Biolegend | RRID: AB_2800961; Cat#356021 |
| CXCR6 BV421 (K041E5) | BioLegend | RRID: AB_2563873; Cat#356014 |
| EOMES PE/eFluor610 (WD1928) | eBiosciences | RRID:; Cat#61-4877-42 |
| FC Blocking Reagent | Miltenyi | RRID: AB_2892112; Cat#130-059-901 |
| FcERJa FITC (AER-37) | Biolegend | RRID: AB_1227653; Cat#334608 |
| GM-CSF PE (BVD2-21C11) | BioLegend | RRID: AB_2085532; Cat#502306 |
| Grz B PE (GB11) | BD Biosciences | RRID: AB_10561690; Cat#561142 |
| Hobit (ZNF683) AF647 (Sanquin-Hobit/1) | BD Biosciences | RRID: AB_2739629; Cat#566250 |
| IFNg BV421 (4S.B3) | Biolegend | RRID: AB_2561398; Cat#502532 |
| IL1R1 PE (polyclonal) | Biotechne | RRID: AB_2124912; Cat#FAB269P-100 |
| IL2 (MQ1-17H12) | Biolegend | RRID: AB_2563878; Cat#500334 |
| IL22 APC (REA466) | Miltenyi | RRID: AB_2652429; Cat#130-106-959 |
| Ki-67 BV421 (Ki-67) | Biolegend | RRID: AB_2563860; Cat#350506 |
| KLRG1 A0153 | Biolegend | RRID: AB_2750373; Cat#367721 |
| KLRG1 BV785 (2F1/KLRG1) | Biolegend | RRID: AB_2629749; Cat#138429 |
| KLRG1 PE/Dazzle 594 (368,608) | Biolegend | RRID: AB_2572135; Cat#368608 |
| NKp30 711 (p30-15) | BD Biosciences | RRID: AB_2738169; Cat#563383 |
| Nkp30 PE (P30-15) | Biolegend | RRID: AB_756111; Cat#325207 |
| NKp44 BV786 (P44-8) | BD Biosciences | RRID: AB_2742134; Cat#744304 |
| Nkp80 A0923 | Biolegend | RRID: AB_2814274; Cat#346709 |
| NKp80 APCVio770 (REA845) | Miltenyi | RRID: AB_2653031; Cat#130-112-593 |
| NKp80 FITC (4A4.D10) | Miltenyi | RRID: AB_10829948; Cat#130-094-843 |
| Nkp80 PE (REA845) | Miltenyi | RRID: AB_2653022; Cat#130-112-590 |
| Perforin BV421 (dG9) | Biolegend | RRID: AB_2566204; Cat#308122 |
| Perforin Pe-Cy7 (B-D48) | Biolegend | RRID: AB_2571973; Cat#353316 |
| TBET 711 (O4-46) | BD Biosciences | RRID: AB_2738136; Cat#563320 |
| TCRa/b FITC (IP26) | Biolegend | RRID: AB_314644; Cat#306706 |
| TCRy/d FITC (B1) | Biolegend | RRID: AB_1575108; Cat#331208 |
| TNF-a BV785 (FN50) | BD Biosciences | RRID: AB_2738441; Cat#563834 |
| anti-human TGF-b1 | Biolegend | RRID: AB_2810654; Cat#521708 |
| Eomes | R&D Systems | RRID: AB_10569705; Cat#AF6166 |
| CD56 | R&D Systems | RRID: AB_442152; Cat#AF2408 |
| αSMA | ThermoFisher | RRID: AB_2572996; Cat#14-9760-82 |
| CD45 | NovusBio | RRID: AB_2864384; Cat#NBP2-34528 |
| CD3e | Abcam | RRID: AB_1191514; Cat#ab271850 |
| CD94 | biorbyt | RRID: AB_2922808; Cat#orb308626 |
| CD32 | BioLegend | RRID: AB_314333; Cat#303201 |
| CD36 | Miltenyi | RRID: AB_2819615; Cat#130-124-322 |
| KLRG1 | Miltenyi | RRID: AB_2889702; Cat#130-126-458 |
| mouse IgG | Sigma | RRID: AB_1163670 I; Cat#5381 |
| Chemicals, peptides, and recombinant proteins | ||
| IL2(IS) | Miltenyi | Cat#130-097-748 |
| IGF-β1 | Miltenyi | Cat#130-095-066 |
| IL-7 | Miltenyi | Cat#130-095-363 |
| IL-15 | Immunotools | Cat#11340155 |
| IL-12 | Immunotools | Cat#11349125 |
| Viability Zombie Green | Biolegend | Cat#423112 |
| viability Zombie-Aqua | Biolegend | Cat#423102 |
| FLT3L | Immunotools | Cat#11343303 |
| Medium F-12 Nut Mix (+) L-Glutamin | Gibco Life | Cat#21765-029 |
| Antibiotic-Antimyotic | Gibco Life | Cat#15240-062 |
| Human Serum AB Plasma | Sigma | Cat#H3667-100mL |
| Sodium Selenite | Sigma (Merck) | Cat#S5261 |
| 2- Mercaptoethanol | Gibco Life | Cat#31350-010 |
| Ascorbic Acid | European Pharmacopoeia Reference | Cat#A1300000 |
| DMEM | Gibco Life | Cat#41965 |
| Penicillin/Streptomycin | PAN | Cat#P06-07100 |
| Fetal bovine serum low in endotoxin A.H. | Sigma | Cat#F7524-500mL |
| Deposited data | ||
| scRNASeq data from Heinrich et al.23 | re-analyzing external dataset | GEO: GSE179795 |
| scRNASeq data batch 1 | This paper | GEO: EGAS00001006847 |
| scRNASeq data batch 2 | This paper | GEO: EGAS00001006847 |
| scRNASeq data tissue batch 1&2 | This paper | GEO: EGAS00001006847 |
| Experimental models: Cell lines | ||
| Human LSECs | ScienCell | Cat#5000 |
| Human Hepatocytes | ScienCell | Cat#5200 |
| Human Hepatic Stellate Cells | ScienCell | Cat#5300 |
| Human Umbilical Vein Endothelial Cells | ScienCell | Cat#8000 |
| Oligonucleotides | ||
| Costumized primer Oligos for qPCR are listed in Table S4 and are all tested for product length by gel electrophoresis | IDT | N/A |
| TrueBlack® Lipofuscin Autofluorescence Quencher | Biotium | Cat#23007 |
| Ultra Filters | Amicon | N/A |
| salmon sperm DNA | Thermo Fisher | Cat#AM9680 |
| MWCO filter columns | ThermoFisher | Cat#UFC505096 |
| Software and algorithms | ||
| Prism 9 | Graphpad | N/A |
| Excel 2011 | Microsoft | N/A |
| Powerpoint 2001 | Microsoft | N/A |
| Cellranger mkfastq 3.0.2 | 10X Genomics | N/A |
| R package Seurat 3.1.1 | cran.r-project.org | N/A |
| NormalizeData | Function R package | N/A |
| FindVariableFeatures | Function R package | N/A |
| ScaleData | Function R package | N/A |
| FindClusters | Function R package | N/A |
| FindAllMarkers | Function R package | N/A |
| AddModuleScore | Function R package | N/A |
| CellphoneDB 2.0.0 | Function R package | N/A |
| FindMarkers | Function R package | N/A |
| FlowJo 10.7.1 | BD Bioscience | N/A |
| Affinity Designer 2.0 | Affinity tools | N/A |
| Affinity Publisher 2.0 | Affinity tools | N/A |
| HALO® Image Analysis software ( | Indica Labs | N/A |
| CODEX® instrument manager software (Akoya Biosciences | Akoya | N/A |
| Other | ||
| Axio Observer 7 inverted microscope | Zeiss | N/A |
| CODEX® instrument | Akoya | N/A |
| multicycle CO-Detection by IndEXing | Akoya | N/A |