KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| LXRα/β | Santa Cruz Biotechnology | Cat#sc-1000X; RRID: AB_632067 |
| LXRβ | Santa Cruz Biotechnology | Cat#sc-133221X RRID: AB_2154783 |
| LXRα/β | Santa Cruz Biotechnology | Cat#sc-271064X RRID: AB_10611071 |
| SMAD4 | Cell Signaling Technology | Cat#46535 RRID: AB_2736998 |
| SMAD4 | Cell Signaling Technology | Cat#38454 RRID: AB_2728776 |
| RBPJ | Abcam | Cat#ab25949 RRID: AB_778155 |
| CD115_PE | BioLegend | Cat#135506; RRID: AB_1937253 |
| CD115_PerCP-eFluor710 (clone AFS998) | eBioscience | Cat#46-1152-82; RRID: none |
| CD11b_BUV395 (clone m1/70) | BD Biosciences | Cat#565976; RRID: none |
| CD11b_PE/Cy7 | BD Biosciences | Cat#552850; RRID: AB_394491 |
| CD11b_PE/Cy7 | BioLegend | Cat#101216; RRID: AB_312799 |
| CD11c_BV605 | BioLegend | Cat#117334; RRID: AB_2562415 |
| CD14_PE | BioLegend | Cat#301806; RRID: AB_314188 |
| CD146_BUV395 (clone ME-9F1) | BD Biosciences | Cat#740330; RRID: none |
| CD16/32 | BioLegend | Cat#101302; RRID: AB_312801 |
| CD16/32 | BD Biosciences | Cat#553142; RRID: AB_394657 |
| CD19_BUV737 (clone 1D3) | BioLegend | Cat#564296; RRID: none |
| CD19_BV711 | BioLegend | Cat#563157; RRID: AB_2738035 |
| CD31_BUV737 (clone MEC 13.3) | BD Biosciences | Cat#565097; RRID: none |
| CD31_BV786 (clone MEC 13.3) | BD Biosciences | Cat#740870; RRID: none |
| CD45_Alexa488 | BioLegend | Cat#103122; RRID: AB_493531 |
| CD45_Alexa488 | BioLegend | Cat#304017; RRID: AB_389314 |
| CD45_Alexa647 | BioLegend | Cat#103124; RRID: AB_493533 |
| CD45_APC/Cy7 | BioLegend | Cat#103116; RRID: AB_312981 |
| CD45_BB515 | BD Biosciences | Cat#564590; RRID: none |
| CD90.2_BV785 | BioLegend | Cat#105331; RRID: AB_2562900 |
| CD3_BV711 | BioLegend | Cat#563123; RRID: AB_2687954 |
| F4/80_BV421 | BioLegend | Cat#123132; RRID: AB_11203717 |
| F4/80_PE | BioLegend | Cat#123110; RRID: AB_893486 |
| F4/80_eFluor450 | Thermo Fisher Scientific | Cat#48480182; RRID: AB_1548747 |
| Ly6C_APC/Cy7 | BioLegend | Cat#128026; RRID: AB_10640120 |
| Ly6C_BV785 | BioLegend | Cat#128041; RRID: AB_2565852 |
| Ly6C_Alexa488 | BioLegend | Cat#128022; RRID: AB_10639728 |
| Ly6G_BV650 | BioLegend | Cat#127641; RRID: AB_2565881 |
| Ly6G_FITC | BioLegend | Cat#127606; RRID: AB_1236494 |
| Ly6G_PE/Dazzle594 | BioLegend | Cat#127648; RRID: AB_2566319 |
| STAB2_Alexa488 (clone D317-A48)) | MBL | Cat#D317-A48; RRID: none |
| Tim4_Alexa647 | BioLegend | Cat#130008; RRID: AB_2271648 |
| Tim4_PE | BioLegend | Cat#130006; RRID: AB_2201843 |
| I-A/I-E_Alexa700 | BioLegend | Cat#107622; RRID: AB_493727 |
| I-A/I-E_Alexa488 | BioLegend | Cat#107616; RRID: AB_493523 |
| Nkp46_BV711 | BioLegend | Cat#137621; RRID: AB_2563289 |
| InVivoMAb anti-mouse DLL1 | BioXcell | Cat#BE0155; RRID: AB_10950546 |
| InVivoMAb anti-mouse DLL4 | BioXcell | Cat#BE0127; RRID: AB_10950366 |
| InVivoMAb polyclonal American hamster IgG | BioXcell | Cat#BE0091; RRID: AB_1107773 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Minimum Essential Medium Eagle | Sigma | Cat#M8042 |
| FBS | Biowest | Cat#S1620 |
| Penicillin-Streptomycin-Glutamine (100X) | Thermo Fisher Scientific | Cat#10378016 |
| Penicillin-Streptomycin | Thermo Fisher Scientific | Cat#15140122 |
| Amphotericin B | Thermo Fisher Scientific | Cat#15290018 |
| mouse M-CSF | Shenandoah Biotech | Cat#200-08 |
| KOD Xtreme Hot Start DNA polymerase | Sigma | Cat#71975 |
| KAPA SYBR FAST qPCR Master mix (2X) | Kapa Biosystems | Cat#07959427001 |
| Dynabeads Protein A | Thermo Fisher Scientific | Cat#10002D |
| Dynabeads Protein G | Thermo Fisher Scientific | Cat#10004D |
| SpeedBeads magnetic carboxylate modified particles | GE Healthcare | Cat#65152105050250 |
| TRIzol Reagent | Thermo Fisher Scientific | Cat#15596018 |
| Formaldehyde | Thermo Fisher Scientific | Cat#BP531-500 |
| Glycine | Thermo Fisher Scientific | Cat#BP3815 |
| DSG Crosslinker | ProteoChem | Cat#c1104-100mg |
| Oligo d(T)25 Magnetic Beads | NEB | Cat#S1419S |
| DTT | Thermo Fisher Scientific | Cat#P2325 |
| SUPERase-In | Ambion | Cat#AM2696 |
| Oligo dT primer | Thermo Fisher Scientific | Cat#18418020 |
| Agencourt RNA Clean XP Beads | Beckman Coulter | Cat#A63987 |
| 10 X Blue Buffer | Enzymatics | Cat#P7050L |
| DNA polymerase I | Enzymatics | Cat#P7050L |
| Random primers | Thermo Fisher Scientific | Cat#48190011 |
| SuperScript III Reverse Transcriptase | Thermo Fisher Scientific | Cat#18080044 |
| 5 X first-strand buffer | Thermo Fisher Scientific | Cat#18080044 |
| Actinomycin D | Sigma | Cat#A1410 |
| Alt-R S.p. Cas9 Nuclease V3 | Integrated DNA Technologies | Cat#1081058 |
| Alt-R CRISPR-Cas9 crRNA | Integrated DNA Technologies | N/A |
| Alt-R CRISPR-Cas9 tracrRNA | Integrated DNA Technologies | Cat#1072532 |
| IDTE pH 7.5 (1X TE Solution) | Integrated DNA Technologies | Cat#11-01-02-02 |
| Diphtheria Toxin from Corynebacterium diphtheriae | Sigma | Cat#D0564 |
| Flavopiridol hydrochloride hydrate | Sigma | Cat#F3055 |
| OptiPrep Density Gradient Medium | Sigma | Cat#D1556 |
| Liberase TM Research Grade | Sigma | Cat#5401127001 |
| Recombinant human DLL4 | R&D systems | Cat#1506-D4-050 |
| Human Transforming Growth Factor β1 (hTGF-β1) | Cell Signaling Technology | Cat#8915LC |
| NEBNext High-Fidelity 2X PCR Master Mix | NEB | Cat#M0541L |
| DAPT | Cell Signaling Technology | Cat#15020S |
| LY411575 | Sigma | Cat#SML0506-25MG |
| Collagenase, Type 1 | Worthington | Cat# LS004196 |
| Hoechst 33342 Solution (20 mM) | Thermo Fisher Scientific | Cat# 62249 |
| Collagenase D | Sigma | Cat# 11088882001 |
| Dispase | Thermo Fisher Scientific | Cat# 17105-041 |
| DNAse | Sigma | Cat# DNA25-100mg |
| Critical Commercial Assays | ||
| Direct-zol RNA MicroPrep Kit | Zymo Research | Cat#R2062 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher Scientific | Cat#Q32851 |
| In-Fusion HD Cloning plus Kit | Clontech | Cat#638909 |
| Nextera DNA Library Prep Kit | Illumina | Cat#FC-121-1030 |
| NEBNext Ultra II DNA library prep kit | NEB | Cat#E7645L |
| NEXTflex DNA Barcodes | Bioo Scientific | Cat#NOVA-514104 |
| ChIP DNA Clean and Concentrator Kit | Zymo Research | Cat#D5205 |
| EasySep Mouse Monocyte Isolation Kit | STEMCELL Technologies | Cat#19861 |
| Deposited Data | ||
| RAW and analyzed data | GEO | GSE128662 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Clec4f-cre-tdTomato | Glass Lab | This study (JAX:033296). |
| Mouse: C57BL/6J | The Jackson Laboratory | RRID: IMSR_JAX:000664 |
| Mouse: Rosa26-Lox-Stop-Lox-DTR (Rosa26iDTR) | The Jackson Laboratory | RRID: IMSR_JAX:007900 |
| Mouse: Rosa26-Lox-Stop-Lox-ZsGreen (Ai6) | The Jackson Laboratory | RRID: IMSR_JAX:007906 |
| Mouse: RosanT-nG mouse | The Jackson Laboratory | RRID: IMSR_JAX:023035 |
| Mouse: Lyz2-cre | The Jackson Laboratory | RRID: IMSR_JAX:004781 |
| Mouse: Smad4fl/fl | The Jackson Laboratory | RRID: IMSR_JAX:017462 |
| Mouse: Nr1h3−/− | The Jackson Laboratory | RRID: IMSR_JAX:013763 |
| Mouse: Nr1h3fl/fl | Chambon Lab | N/A |
| Oligonucleotides | ||
| Smad4_qF1 | CAGCCTCCCATTTCCAATCATC | |
| Smad4_qR1 | CGAAGGATCCACATAGCCATCC | |
| 18s_qF | AATTCCCAGTAAGTGCGGGTCA | |
| 18s_qR | GATCCGAGGGCCTCACTAAACC | |
| Recombinant DNA | ||
| Clec4f targeting vector | Glass Lab | This study |
| Software and Algorithms | ||
| Bowtie2 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| STAR | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| Irreproducibility Discovery Rate (IDR) | (Li et al., 2011) | https://www.encodeproject.org/software/idr/ |
| HOMER | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/ |
| R package: DEseq2 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| R package: pheatmap | N/A | https://www.rdocumentation.org/packages/pheatmap/versions/1.0.10/topics/pheatmap |
| pygbrowse | N/A | https://github.com/phageghost/python-genome-browser |
| Ingenuity Pathway Analysis | N/A | https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ |
| GraphPad Prism | GraphPad Software, Inc., California | |
| FlowJo | FlowJo LLC, Ashland, Oregon | |
| Imaris | Bitplane | |