Reagent/Resource	Reference or Source	Identifier or Catalog Number
Acta1GFP/+	CMV–β‐actin hybrid promoter, Ajami et al 2007
Ccr2RFP/+	B6.129(Cg)‐Ccr2tm2.1Ifc/J (Stock No: 017586, JAX mice)
Cx3cr1GFP/+	B6.129P2(Cg)‐Cx3cr1tm1Litt/J (Stock No: 005582)
Cx3cr1CreERT2	B6.129P2(C)‐Cx3cr1tm2.1(cre / ERT2)Jung/J (Stock No: 020940)
Flt3‐Cre	Benz et al 2008
HexbtdT/tdT	Masuda et al 2020
Itgax‐DTR/EGFP	B6.FVB‐1700016L21RikTg(Itgax‐DTR / EGFP)57Lan/J (Stock No. 004509, JAX mice)
Rosa26‐fl‐stop‐fl‐tdTomato	B6.Cg‐Gt(ROSA)26Sortm9(CAG‐tdTomato)Hze/J ( Stock No: 007909, JAX mice)
Rosa26‐fl‐stop‐fl‐EYFP	B6.129X1‐Gt(ROSA)26Sortm1(EYFP)Cos/J (Stock No: 006148, JAX mice)
Antibodies
rabbit anti‐Iba‐1, polyclonal, 1:500 (cryo) or 1:1000 (flat‐mount)	WAKO, Osaka, Japan	cat # 019‐19741
rabbit anti‐Iba‐1, polyclonal, 1:500 (cryo) or 1:1000 (flat‐mount)	Synaptic Systems, Göttingen, Germany	cat # 234 013
rabbit anti‐P2RY12, polyclonal, 1:500	AnaSpec, Fremont, USA	cat # AS‐55043A
rabbit anti‐Tmem119, polyclonal, 1:500	Synaptic Systems, Göttingen, Germany	cat # 400 002
rat anti‐MHC class II (clone M5.114.15.2), monoclonal, 1:500	BioLegend, USA	cat # 107602
goat anti‐GFP, polyclonal, 1:1000	Rockland Immunochemicals Inc., Gilbertsville, USA	cat # 600‐106‐215
goat anti‐GFP, polyclonal, 1:1000	Acris Antibodies Inc., San Diego, USA	cat # R1091P
rat anti‐CD74‐Alexa Flour® 647 (clone In1/CD74), monoclonal, 1:100	BioLegend, USA	cat # 151003
rat anti‐CD206‐Alexa Flour® 647 (clone MR5D3), monoclonal, 1:100	Bio‐Rad Laboratories, UK	cat # MCA2235A647
rat anti‐F4/80 (clone BM8), monoclonal, 1:100	Abcam plc., UK	cat# ab16911
donkey anti‐rabbit, Alexa Fluor 568®, polyclonal, 1:500	Thermo Fisher Scientific Inc., USA	cat # A10042
donkey anti‐goat Alexa Fluor 647®, polyclonal, 1:500	Thermo Fisher Scientific Inc., USA	cat # A‐21447
goat anti‐rabbit, Alexa Fluor 647®, polyclonal, 1:500	Thermo Fisher Scientific Inc., USA	cat # A‐21244
goat anti‐rat, Alexa Fluor 568®, polyclonal, 1:500	Thermo Fisher Scientific Inc., USA	cat # A‐11077
goat anti‐rat, Alexa Fluor 647®, polyclonal, 1:500	Thermo Fisher Scientific Inc., USA	cat # A‐21247
mouse anti‐HLA‐DP, DQ, DR, (clone CR3/43), monoclonal, 1:200	Agilent Dako, Santa Clara, CA, USA)	cat # M0775
Fc receptor blocking antibody CD16/CD32 (clone 2.4G2)	BD Pharmingen, BD Biosciences, Heidelberg, Germany	cat # 553141
rat anti‐CD11b‐BV421 (clone M1/70), monoclonal, 1:100	BioLegend, USA	cat # 101235
rat anti‐CD45‐APC‐e780 (clone 30‐F11), monoclonal, 1:100	Thermo Fisher Scientific Inc., USA	cat # 47‐0451‐82
rat anti‐CD115‐PE‐Cy7 (AFS98), monoclonal, 1:100	Thermo Fisher Scientific Inc., USA	cat # 25‐1152‐82
rat anti‐F4/80‐PE‐Cy7 (BM8), monoclonal, 1:100	Thermo Fisher Scientific Inc., USA	cat # 25‐4801‐82
mouse anti‐CD64‐Alexa647 (clone, X54‐5/7.1), monoclonal, 1:100	BioLegend, USA	cat # 139322
rat anti‐Ly6C‐FITC (clone AL‐21), monoclonal, 1:100	BD Pharmingen, BD Biosciences, Heidelberg, Germany	cat # 553104
rat anti‐Ly6G‐PE‐Cy7 (clone 1A8), monoclonal, 1:100	BD Pharmingen, BD Biosciences, Heidelberg, Germany	cat # 560601
anti‐CD45‐BV421 (clone 30‐F11), monoclonal, 1:100	BioLegend, USA	cat # 103134
rat anti‐CD3‐PE‐Cy7 (clone 17A2), monoclonal, 1:100	BioLegend, USA	cat # 100220
rat anti‐CD19‐PE‐Cy7 (clone 6D5), monoclonal, 1:100	BioLegend, USA	cat # 115519
Oligonucleotides and other sequence‐based reagents
RNAprotect Tissue Reagent	QIAGEN, Hilden, Germany	cat # 76104
RNeasy Plus Micro Kit	QIAGEN, Hilden, Germany	cat # 74034
Buffer RLT Plus	QIAGEN, Hilden, Germany	cat # 1053393
SMARTer Ultra Low Input RNA Kit for Sequencing v4	Clontech Laboratories, Inc., Mountain View, CA, USA	cat # 634456
KAPA SYBR FAST ABI Prism Library Quantification Kit	Roche, Basel, Switzerland	cat # KK4835
Illumina TruSeq SR Cluster Kit v3	Illumina, USA	cat # GD‐401‐3001
TruSeq SBS v3 Reagents	Illumina, USA	cat # FC‐401‐3001
AMPure/RNAClean XP beads	Beckman Coulter, München, Germany	cat # A63987
Quick‐RNA FFPE Kit	Zymo Research, USA	cat # R1008
DNAse I digestion using the Baseline‐ZERO kit	Lucigen Corporation, USA	cat # DB0715K
Qubit RNA HS Assay Kit	Thermo Fisher Scientific Inc., USA	cat # Q32852
RNA Pico Sensitivity Assay	Perkin Elmer, USA	cat # CLS960012
Chemicals, enzymes and other reagents
Fluorescein	Alcon Pharma GmbH	cat # H12588‐0113
Tissue‐Tek® O.C.T.TM Compound	Sakura Finetek Germany GmbH	cat # 4583
in Vitro‐Clud® (R. Langenbrinck GmbH, Emmendingen, Germany).	R. Langenbrinck GmbH, Emmendingen, Germany	cat # 04‐0001
May‐Grünwald (Merck 101424)	Merck	cat # 101424
Giemsa (Merck 109204)	Merck	cat # 109204
Tamoxifen (TAM, T5648‐1G, Sigma‐Aldrich, Taufkirchen, Germany)	Sigma‐Aldrich, Taufkirchen, Germany	cat # T5648‐1G
corn oil (Sigma‐Aldrich, C8267‐500ml)	Sigma‐Aldrich, Taufkirchen, Germany	cat # C8267‐500ml
Hank's Balanced Salt Solution	Thermo Fisher Scientific Inc., USA	cat # 14170138
eBioscience™ Fixable Viability Dye eFluor™ 506	Thermo Fisher Scientific Inc., USA	cat # 65‐0866‐14
eBioscience™ Fixable Viability Dye eFluor™ 780	Thermo Fisher Scientific Inc., USA	cat # 65‐0865‐18
Software
FACSDiva software	BD Biosciences, Heidelberg, Germany
FlowJo software (7.6.1)	Treestar (BD Biosciences, Heidelberg, Germany)
IMARIS 8.0	Bitplane, Switzerland
FV10‐ASW 4.2 Viewer	Olympus, Tokyo, Japan
GraphPad Prism (Version 6.0)	GraphPad Software, USA
Other
RS 2000 Biologica x‐Ray irradiator	Rad Source Technologies, USA
VISULAS 532s	Carl Zeiss Meditec AG, Jena, Deutschland
Olympus BX‐61 fluorescence microscope	Olympus, Tokyo, Japan
Olympus DP71 color camera	Olympus, Tokyo, Japan
BZ‐9000 fluorescence microscope	Keyence, Osaka, Japan
Fluoview FV 1000 confocal microscope	Olympus, Tokyo, Japan
20x 0.95 NA XLUMPlanFL N objective	Olympus, Tokyo, Japan
20x 0.75 NA U Plan S Apo objective	Olympus, Tokyo, Japan
40x 0.95 NA U Plan S Apo objective	Olympus, Tokyo, Japan
DMi‐8 confocal microscope	Leica, Wetzlar, Germany
20x NA 0.75 CS2 objective	Leica, Wetzlar, Germany
FACSCanto II	BD Biosciences, Heidelberg, Germany
FACSAria III	BD Biosciences, Heidelberg, Germany
MoFlo High Speed Cell Sorter	Beckman Coulter, München, Germany
HiSeq 3000	Illumina, USA
HiSeq 1000	Illumina, USA
NextSeq 500	Illumina, USA
mosquito® HTS Nanolitre Liquid Handler	SPT Labtech, USA
Autostainer	Agilent Dako, Santa Clara, CA, USA
Qubit Fluorometer	Life Technologies, USA
LabChip GXII Touch	Perkin Elmer, USA
384‐well plates	Biorad, Munich, Germany
RNeasy Plus Micro Kit	QIAGEN, Hilden, Germany	cat # 74034
Click‐iT® EdU Alexa Fluor® 488 Imaging Kit	Thermo Fisher Scientific	cat # C10337
Dako REALTM EnVisionTM Detection System Kit	Agilent Dako, Santa Clara, CA, USA	cat # K406511‐2