| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat anti-CD68 | Bio-Rad | Cat# MCA1957; RRID:AB_322219 |
| Rabbit anti-FN1 | Millipore | Cat# AB2033; RRID:AB_2105702 |
| Goat anti-FOXP2 | Santa Cruz Biotechnology | Cat# sc-21069; RRID:AB_2107124 |
| Chicken anti-GFP | Aves Labs | Cat# GFP-1020; RRID:AB_10000240 |
| Rabbit anti-IBA1 | FUJIFILM Wako Shibayagi | Cat# 019-19741; RRID:AB_839504 |
| Rabbit anti-IBA1 (human) | Abcam | Cat# ab178846; RRID:AB_2636859 |
| Chicken anti-IBA1 | Synaptic Systems | Cat# 234009; RRID:AB_2891282 |
| Rat anti-Lgals3 (MAC2) | CEDARLANE | Cat# CL8942AP; RRID:AB_10060357 |
| Rat anti-L1 | Millipore | Cat# MAB5272; RRID:AB_2133200 |
| Biotinylated rat anti-LYVE1 | Thermo Fisher Scientific | Cat# 13-0443-82; RRID:AB_1724157 |
| Rat anti-Myelin Basic Protein (MBP) | Millipore | Cat# MAB386; RRID:AB_94975 |
| Rat anti-mDectin-1 (CLEC7A) | InvivoGen | Cat# mabg-mdect; RRID:AB_2753143 |
| Mouse anti-neurofilament marker SMI-312 | BioLegend | Cat# 837904; RRID:AB_2566782 |
| Goat anti-mouse Osteoactivin (GPNMB) | R and D Systems | Cat# AF2330; RRID:AB_2112934 |
| Rabbit anti-P2Y12 receptor | AnaSpec; EGT Group | Cat# 55043A; RRID:AB_2298886 |
| Goat anti-SPP1 | R and D Systems | Cat# AF808; RRID:AB_2194992 |
| Donkey anti-chicken Alexa 10 Fluor® 488-conjugated | Jackson ImmunoResearch Labs | Cat# 703-545-155; RRID:AB_2340375 |
| Donkey anti-goat Alexa 10 Fluor® 488-conjugated | Jackson ImmunoResearch Labs | Cat# 705-545-147; RRID:AB_2336933 |
| Donkey anti-rat Alexa 10 Fluor® 488-conjugated | Jackson ImmunoResearch Labs | Cat# 712-545-150; RRID:AB_2340683 |
| Donkey anti-rabbit Alexa 10 Fluor® 488-conjugated | Jackson ImmunoResearch Labs | Cat# 711-545-152; RRID:AB_2313584 |
| Donkey anti-goat Cy3-conjugated | Jackson ImmunoResearch Labs | Cat# 705-165-147; RRID:AB_2307351 |
| Donkey anti-rabbit Cy3-conjugated | Jackson ImmunoResearch Labs | Cat# 711-165-152; RRID:AB_2307443 |
| Donkey anti-rat Cy3-conjugated | Jackson ImmunoResearch Labs | Cat# 712-165-150; RRID:AB_2340666 |
| Donkey anti-goat Alexa 10 Fluor® 647-conjugated | Jackson ImmunoResearch Labs | Cat# 705-605-147; RRID:AB_2340437 |
| Donkey anti-goat Cy5-conjugated | Jackson ImmunoResearch Labs | Cat# 705-175-147; RRID:AB_2340415 |
| Donkey anti-rat Cy5-conjugated | Jackson ImmunoResearch Labs | Cat# 712-175-150; RRID:AB_2340671 |
| Biological samples | ||
| Human fetal brain tissue | Gynaecology Department, Jeanne de Flandre Hospital, Lille, France | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Lipopolysaccharide | InvivoGen | Cat# tlrl-pelps; CAS: 93572-42-0 |
| Pexidartinib (PLX3397) | Plexxikon | CAS: 1029044-16-3 |
| Anti-CSF1R mAb (αCSF1R, clone AFS98) | Florent Ginhoux laboratory | N/A |
| Triton 100X | Eurobio | Cat# GAUTTR00-07 |
| Hoechst | Sigma Aldrich | Cat# 33342 |
| Paraformaldehyde | Sigma Aldrich | Cat# P6148 |
| Gelatin | VWR chemical | Cat# 24350.262 |
| Dibenzylether | Sigma Aldrich | Cat# 33630 |
| Dichloromethane | Sigma Aldrich | Cat# 270997 |
| Methanol | Sigma Aldrich | Cat# 34860 |
| Critical commercial assays | ||
| BD™ Ms Single Cell Sample Multiplexing Kit | BD Biosciences | Cat# 633793 |
| BD Rhapsody™ Whole Transcriptome Analysis (WTA) Amplification Kit | BD Biosciences | Cat# 633801 |
| BD Rhapsody™ Whole Transcriptome Analysis (WTA) Reagent Kit | BD Biosciences | Cat# 665915 |
| pHrodo™ BioParticles™ Conjugates for Phagocytosis and Phagocytosis Kit | Thermo Fisher Scientific | Cat# P35361 |
| Deposited data | ||
| scRNA-seq for embryonic microglia (C57BL/6) | La Manno et al.30 | http://mousebrain.org/development (“dev_all.loom”) |
| scRNA-seq for postnatal microglia (C57BL/6) | Hammond et al.22 | GSE: 121654 |
| scRNA-seq for postnatal microglia (C57BL/6) | Li et al.21 | GSE: 123025 |
| scRNA-seq for Spp1-/- and +/+ (C57BL/6) | This study | ArrayExpress accession E-MTAB-13581 https://www.ebi.ac.uk/biostudies/arrayexpress |
| Experimental models: Organisms/strains | ||
| Mouse: Cx3cr1gfp/+ | The Jackson Laboratory | RRID:IMSR_JAX:005582 |
| Mouse: Pu.1+/− | Back et al.52 | N/A |
| Mouse: Cd11c-eYFP | The Jackson Laboratory | RRID:IMSR_JAX:007567 |
| Mouse: Spp1-/- | The Jackson Laboratory | RRID:IMSR_JAX:004936 |
| Mouse: Csf1rΔFIRE/+ | Rojo et al.53 | RRID:IMSR_JAX:032783 |
| Mouse: Cd11b−/− | The Jackson Laboratory | RRID:IMSR_JAX:003991 |
| Mouse: Dap12/TyroBP−/− | Tomasello et al.94 | RRID:MGI:3818477 |
| Mouse: RhoAfl/fl | Jackson et al.95 | N/A |
| Mouse: Emx1cre/+; RhoAfl/+ | Cappello et al.63 | N/A |
| Mouse: WntA3dta/+; Brn4cre/+ | Deck et al.64 | N/A |
| Mouse: C57BL/6J | The Jackson Laboratory | Cat# 000664; RRID: IMSR_JAX:000664 |
| Software and algorithms | ||
| FIJI (ImageJ) 1.50 g | National Institute of Health | https://fiji.sc/; https://imagej.nih.gov/ij/index.html; RRID: SCR_003070 |
| LAS AF 4.0 | Leica Microsystems |
https://www.leica-microsystems.com/; RRID: SCR_013673 |
| GraphPad Prism 9.5 | GraphPad Software | RRID: SCR_000306 |
| Adobe Photoshop CS6 | Adobe Systems | RRID: SCR_014199 |
| Adobe Illustrator CS6 | Adobe Systems | RRID: SCR_010279 |
| R software 4.2.2 | GNU Project | https://www.r-project.org/; RRID:SCR_001905 |
| R package: Metascape 3.5.20230501 | Metascape Team | http://metascape.org/gp/index.html#/main/step1; RRID:SCR_016620 |
| R package: Seurat 4.3.0.1 | N/A | https://satijalab.org/seurat/get_started.html; RRID:SCR_016341 |
| R package: Tidyverse 2.0.0 | N/A |
https://CRAN.R-project.org/ package=tidyverse ; RRID:SCR_019186 |
| R package: Viridis 0.6.4 | N/A | https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html ; RRID:SCR_016696 |
| R package: Clustree 0.5.0 | N/A | https://CRAN.R-project.org/package=clustree ; RRID:SCR_016293 |
| R package: EnhancedVolcano 1.16.0 | N/A | https://bioconductor.org/packages/EnhancedVolcano/ ; RRID:SCR_018931 |
| R package: Paletteer 1.5.0 | N/A | https://CRAN.R-project.org/package=paletteer |
| R package: Ggplot2 3.4.3 | N/A | https://cran.r-project.org/web/packages/ggplot2/index.html ; RRID:SCR_014601 |
| R package: Sctransform 0.3.5 | N/A | https://github.com/satijalab/sctransform ; RRID:SCR_022146 |
| R package: GlmGamPoi 1.10.2 | N/A | https://bioconductor.org/packages/glmGamPoi/ |
| Bowtie 2 | N/A | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ; RRID:SCR_016368 |
| Illumina HiSeq 4000 system | Ilumina | https://www.illumina.com/systems/sequencing-platforms/hiseq-3000-4000.html ; RRID:SCR_020127 |
| Rhapsody analysis pipeline | BD Biosciences | https://www.bdbiosciences.com |
| t-SNE | GitHub | https://github.com/jkrijthe/Rtsne |
| UMAP | GitHub | https://github.com/lmcinnes/umap |
| Imaris x64 software version 10.0 | Bitplane | RRID:SCR_007370 |
| Imspector Pro software | Miltenyi BioTec | https://www.miltenyibiotec.com |
| Gatan DigitalMicrograph software | Gatan | https://www.gatan.com |
| pClamp 10.3 software | Molecular devices | https://support.moleculardevices.com |
| Other | ||
| Leica TCS-SP8 confocal microscope | Leica | https://www.leica-microsystems.com/ |
| Leica TCS SP5 confocal microscope | Leica | https://www.leica-microsystems.com/ |
| Ultramicroscope II lightsheet microscope | Miltenyi BioTec | https://www.miltenyibiotec.com |
| Leica DMi8 fluorescence microscope | Leica | https://www.leica-microsystems.com/ |
| Philips Tecnai 12 Transmission Electron Microscope | Philips/FEI | https://nano.tau.ac.il |
| Leica CM 3050S cryostat | Leica | https://www.leica-microsystems.com/ |
| Olympus BX51WIF microscope | Olympus | https://www.olympus-lifescience.com |
| ssniff standard mouse chow | ssniff Spezialdiäten GmbH | https://www.ssniff.com |
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