Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-APC Antibody | Millipore Sigma | Cat#OP80; RRID: AB_2057371 |
| Anti-BrdU antibody | Abcam | Cat#ab6326; RRID: AB_305426 |
| Anti-CD28 Antibody | Thermo Fisher Scientific | Cat#14-0281; RRID: AB_467191 |
| Anti-CD29 Antibody | Thermo Fisher Scientific | Cat# 14-0291-82; RRID: AB_657727 |
| Anti-CD3e Antibody | Thermo Fisher Scientific | Cat#14-0031; RRID: AB_467050 |
| Anti-GFP Antibody | Thermo Fisher Scientific | Cat#G10362; RRID: AB_2536526 |
| Anti-Iba1Antibody | Abcam | Cat# ab5076; RRID: AB_2224402 |
| Anti-IL-2 Antibody | Thermo Fisher Scientific | Cat#16-7022-85; RRID: AB_469207 |
| Anti-MAP2 Antibody | Santa Cruz | Cat# sc-20172; RRID: AB_2250101 |
| Anti-MBP Antibody | Abcam | Cat# ab40390; RRID: AB_1141521 |
| Anti-NF-H Antibody (SMI32) | BioLegend | Cat# 801701; RRID: AB_2564642 |
| Anti-NG2 Antibody | Millipore Sigma | Cat#AB5320; RRID: AB_11213678 |
| Anti-Osteopontin Antibody | Abcam | Cat#ab8448; RRID: AB_306566 |
| Anti-TGM2 Antibody | R&D Systems | Cat# AF4376; RRID: AB_10890213 |
| Anti-VEGF-A Antibody | Biolegend | Cat# 512809; RRID: AB_2814439 |
| Anti-Arg1 Antibody, APC | R&D Systems | Cat# IC5868A; RRID: AB_2810265 |
| Anti-CD11b Antibody, APC | BioLegend | Cat# 101211; RRID: AB_312794 |
| Anti-CD25 Antibody, Alexa Fluor® 700 | BioLegend | Cat# 102024; RRID: AB_493709 |
| Anti-CD25 Antibody, APC | BioLegend | Cat# 102012; RRID: AB_312861 |
| Anti-CD25 Antibody, PE | Thermo Fisher Scientific | Cat# 12-0251; RRID: AB_465607 |
| Anti-CD29 (Integrin beta 1) Antibody, PE | Thermo Fisher Scientific | Cat#12-0291-81; RRID: AB_657733 |
| Anti-CD3 Antibody, APC-Cy7 | BioLegend | Cat# 100221; RRID: AB_2057374 |
| Anti-CD3 Antibody, FITC | Thermo Fisher Scientific | Cat# 11-0032-80; RRID: AB_2572430 |
| Anti-CD4 Antibody, BUV395 | BD Biosciences | Cat#563790; RRID: AB_2738426 |
| Anti-CD4 Antibody, BV510 | BioLegend | Cat # 100449; RRID: AB_2564587 |
| Anti-CD4 Antibody, ef450 | Thermo Fisher Scientific | Cat# 48-0042; RRID: AB_1272194 |
| Anti-CD45 Antibody, PE-Cyanine5 | Thermo Fisher Scientific | Cat#15-0451-81; RRID: AB_468751 |
| Anti-CD45 Antibody, PE-CF594 | BD Biosciences | Cat#562420; RRID: AB_11154401 |
| Anti-CTLA4 Antibody, BV605 | Biolegend | Cat# 106323; RRID: AB_2566467 |
| Anti-Foxp3 Antibody, APC | Thermo Fisher Scientific | Cat#17-5773-82; RRID: AB_469457 |
| Anti-Foxp3 Antibody, PE-Cy7 | Thermo Fisher Scientific | Cat# 25-5773-82; RRID: AB_891552 |
| Anti-GLAST Antibody, APC | Miltenyi Biotec | Cat# 130-123-555; RRID: AB_2811532 |
| Anti-Helios Antibody, FITC | Biolegend | Cat# 137214; RRID: AB_10662745 |
| Anti-Human and Sheep IgG Fc Antibody, APC-Cy7 | Biolegend | Cat# 409313; RRID: AB_2561858 |
| Anti-IL-10 Antibody, APC-Cy7 | Biolegend | Cat# 505035; RRID: AB_2566330 |
| Anti-O4 Antibody, APC | Miltenyi Biotec | Cat#130-119-155; RRID: AB_2751644 |
| Anti-Osteopontin Antibody, PE | R&D Systems | Cat# IC808P; RRID: AB_10643832 |
| Anti-Rat IgG Antibody, BV421 | Biolegend | Cat# 405414; RRID: AB_10900808 |
| IgG2a kappa Isotype antibody | Thermo Fisher Scientific | Cat#: 16-4321-82; AB_470156 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Diphtheria Toxin | Sigma-Aldrich | Cat#D0564-1MG |
| IL-2, Recombinant Protein | Thermo Fisher Scientific | Cat#34-8021-85 |
| Luxol® Fast Blue MBSN | Sigma-Aldrich | Cat#S3382-25G |
| Osteopontin Protein | R&D Systems | Cat#441OP050CF |
| Percoll | GE Healthcare | Cat#17-0891-01 |
| PLX5622 | Chemgood | Cat#C-1521 |
| (Z)-4-Hydroxytamoxifen | Sigma-Aldrich | Cat#H7904 |
| Critical Commercial Assays | ||
| CD4+CD25+ Regulatory T Cell Isolation Kit, mouse | Miltenyi Biotec | Cat# 130-091-041 |
| Mouse on Mouse (M.O.M.) Basic Kit | Vector laboratories | Cat#BMK-2202 |
| Neural Tissue Dissociation Kit (T) | Miltenyi Biotec | Cat#130-093-231 |
| Nextera XT DNA Library Prep Kit | Illumina | Cat#15031942 |
| RNeasy Plus Micro Kit | Qiagen | Cat#74034 |
| SMART-Seq HT Kit | Takara Bio | Cat#634456 |
| SMART-Seq Ultralow Input RNA Kit | Takara Bio | Cat#634890 |
| UltraComp eBeads Compensation Beads | Thermo Fisher Scientific | Cat#01-2222-42 |
| Deposited Data | ||
| Raw data files for RNA-seq | This paper | GEO: GSE171171 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J (WT) | The Jackson Laboratory | Stock No: 000664 |
| Mouse: Cx3crcre/ER | The Jackson Laboratory | Stock No: 021160 |
| Mouse: Foxp3DTR/GFP | The Jackson Laboratory | Stock No: 016958 |
| Mouse: Itgb1flox/flox | The Jackson Laboratory | Stock No: 004605 |
| Mouse: Rag1−/− | The Jackson Laboratory | Stock No: 002216 |
| Mouse: Spp1−/− | The Jackson Laboratory | Stock No: 004936 |
| Oligonucleotides | ||
| qPCR primer Mbp: | Thermo Fisher Scientific | F:CACAGAAGAGACCCTCACAGCGACA R:CCGCTAAAGAAGCGCCCGATGGA |
| qPCR primer Spp1: | Thermo Fisher Scientific | F:GAATCTCCTTGCGCCACAGAATG R:CATCTGTGGCATCAGGATACTGTTC |
| qPCR primer Gapdh: | Thermo Fisher Scientific | F: TGCTGGTGCTGAGTATGTCGTG R: CGGAGATGATGACCCTTTTGG |
| Software and Algorithms | ||
| Cell Ranger 3.0.1 | 10xGenomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| Chipster 3.15 | CSC-IT Center for Science | https://chipster.csc.fi/ |
| DESeq2 | Bioconductor | http://bioconductor.org/packages/DESeq2/ |
| DSI studio | (Yeh et al., 2013) | http://dsi-studio.labsolver.org/ |
| edgeR 3.26.8 | Bioconductor | http://bioinf.wehi.edu.au/edgeR |
| FastQC | Babraham Bioinformatics | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| FlowJo 10.5.3 | TreeStar FlowJo LLC. | https://www.flowjo.com/ |
| GraphPad Prism 8.4.3 | GraphPad Software | https://www.graphpad.com |
| GSEA 4.0.1 | UC San Diego and Broad Institute | http://gsea-msigdb.org/gsea/index.jsp |
| HTSeq | (Anders et al., 2015) | http://htseq.readthedocs.io/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Imaris 9.3 | Bitplane | https://imaris.oxinst.com/ |
| Ingenuity Pathway Analysis | Qiagen | http://qiagen.force.com/KnowledgeBase/KnowledgeIPAPage |
| pClamp 10 software | Molecular Devices, LLC | https://www.moleculardevices.com/products/axon-patch-clamp-system |
| R 3.5 | R | https://www.r-project.org/ |
| Seurat 2.3.4 | (Stuart et al., 2019) | https://cran.r-project.org/web/packages/Seurat |
| STAR 2.7.8 | GitHub | https://github.com/alexdobin/STAR |
| STRING 11.0 | STRING | https://string-db.org/ |