KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| APC/eFluor 780 anti-mouse CD45 rat monoclonal (Clone 30-F11) | eBioscience | Cat# 47-0451-82 RRID: AB_1548781 |
| Alexa Fluor 700 anti-mouse CD11b rat monoclonal (Clone M1/70) | eBioscience | Cat# 56-0112-82 RRID: AB_657585 |
| eFluor 450 anti-mouse F4/80 rat monoclonal (Clone BM8) | eBioscience | Cat# 48-4801-82 RRID: AB_1548747 |
| PE/Cy7 anti-mouse Ly6G rat monoclonal (clone 1A8) | Biolegend | Cat# 127618 RRID: AB_1877261 |
| APC anti-mouse Ly6C rat monoclonal (clone HK1.4) | eBioscience | Cat# 17–5932 RRID: AB_1724155 |
| Alexa Fluor 488 anti-mouse CD206 rat monoclonal (clone C068C2) | Biolegend | Cat# 141710 RRID: AB_10900445 |
| eFluor 450 anti-mouse MHCII rat monoclonal (clone M5/114.15.2) | eBioscience | Cat# 48-5321-82 RRID: AB_1272204 |
| PE/Cy7 anti-mouse CD11c Armenian hamster monoclonal (clone N418) | Biolegend | Cat# 117318 RRID: AB_493568 |
| APC anti-mouse EpCam rat monoclonal (clone G8.8) | BD Biosciences | Cat# 563478 RRID: AB_2738234 |
| PerCp/Cy5.5 anti-mouse CD64 rat monoclonal (clone X54–5/7.1) | Biolegend | Cat# 139308 RRID: AB_2561963 |
| FITC anti-mouse CD3e Armenian hamster monoclonal (clone 145–2C11) | eBioscience | Cat# 11-0031-82 RRID: AB_464882 |
| PerCp anti-mouse CD4 rat monoclonal (clone GK1.5) | Biolegend | Cat# 100434 RRID: AB_893324 |
| APC anti-mouse CD8a rat monoclonal (clone 53–6.7) | eBioscience | Cat# 17-0081-83 RRID: AB_469336 |
| PE anti-mouse gd-TCR Armenian hamster monoclonal (clone GL3) | BD Biosciences | Cat# 553178 RRID: AB_394689 |
| Alexa Fluor 700 anti-mouse CD29 Armenian hamster monoclonal (clone HMbeta1–1) | Biolegend | Cat# 102218 RRID: AB_493711 |
| Brilliant Violet 421 anti-mouse CD34 rat monoclonal (clone MEC14.7) | Biolegend | Cat# 119321 RRID: AB_10900980 |
| Brilliant Violet 500 anti-mouse Ly-6A/E (SCA1) rat monoclonal (clone D7) | BD Biosciences | Cat# 561229 RRID: AB_10561841 |
| PE/Cy7 anti-mouse CD26 rat monoclonal (clone H194–112) | Biolegend | Cat# 137810 RRID: AB_2564312 |
| Anti-mouse CD45 Alexa Fluor 700 | eBioscience | Cat# 56-0451-82 RRID: AB_891454 |
| APC anti-mouse gdTCR Armenian hamster monoclonal (GL3) | Biolegend | Cat# 118116 RRID: AB_1731813 |
| PE anti-mouse CD3e Armenian hamster (145–2C11) | BD Biosciences | Cat# 553063 RRID: AB_394596 |
| APC-eFluor 780 anti-mouse CD3e Armenian hamster (145–2C11) | eBioscience | Cat# 47-0031-82 RRID: AB_11149861 |
| APC-Fire750 anti-mouse CD31 rat monoclonal (390) | Biolegend | Cat# 102434 RRID: AB_2629683 |
| Rat anti-mouse Foxp3 eFluor 450 | eBioscience | Cat# 48-5773-82 RRID: AB_1518812 |
| Brilliant Violet 650 anti-mouse CD4 | Biolegend | Cat# 100545 RRID: AB_11126142 |
| PE-Cyanine7 rat anti-mouse IL-17A | eBioscience | Cat# 25-7177-80 RRID: AB_10717952 |
| FITC rat anti-mouse IFN (XMG1.2) | eBioscience | Cat# 11-7311-82 RRID: AB_465412 |
| Brilliant Violet 605 anti-mouse CD8a | Biolegend | Cat# 100743 RRID: AB_2561352 |
| Anti-Mouse/Rat CD278 (ICOS) FITC | eBioscience | Cat# 11-9949-80 RRID: AB_465457 |
| PerCP-eFluor 710 anti-mouse CD27 Armenian hamster (LG.7F9) | eBioscience | Cat# 46-0271-82 RRID: AB_1834447 |
| APC anti-mouse CD103 Armenian hamster (2E7) | eBioscience | Cat# 17-1031-82 RRID: AB_1106992 |
| APC anti-rat CD140a (Pdgfra) (APA5) | Biolegend | Cat# 135908 RRID: AB_2043970 |
| Anti-Collagen I rabbit polyclonal | Abcam | Cat# ab34710 RRID: AB_731684 |
| Anti-Collagen III rabbit polyclonal | Abcam | Cat# ab7778 RRID: AB_306066 |
| Anti-Fibrillin 1 rabbit polyclonal | Novus | Cat# NBP1–84723 RRID: AB_11005848 |
| Anti-Fibronectin rabbit polyclonal | Abcam | Cat# ab23750 RRID: AB_447655 |
| Anti-alpha smooth muscle actin rabbit polyclonal | Abcam | Cat# ab5694 RRID: AB_2223021 |
| Anti-Perilipin1 goat polyclonal | Abcam | Cat# ab61682 RRID: AB_944751 |
| Anti-Pparg rabbit monoclonal (clone K.242.9) | Thermo | Cat# MA5–14889 RRID: AB_10985650 |
| Anti-Vimentin rabbit monoclonal (clone D21H3) | Cell Signaling | Cat# 5741 RRID: AB_10695459 |
| Anti-CD31 rat monoclonal (clone MEC13.3) | BD Bioscience | Cat# 550274 RRID: AB_393571 |
| Anti-mouse ITGA6 rat monoclonal (clone GoH3) | R&D Systems | Cat# MAB13501 RRID: AB_2128311 |
| Anti-ER-TR7 rat monoclonal | Abcam | Cat# ab51824 RRID: AB_881651 |
| Anti-GFP chicken polyclonal | Abcam | Cat# ab13970 RRID: AB_300798 |
| Anti-CD68 rabbit polyclonal | Abcam | Cat# ab125212 RRID: AB_10975465 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Diphtheria Toxin | Sigma | D0564 |
| Tamoxifen | Sigma | T5648 |
| LipidTOX | Invitrogen | H34477 |
| Liberase TM | Roche | 05401127001 |
| Sytox Orange | Invitrogen | S34861 |
| Sytox Blue | Invitrogen | S34857 |
| Sybr Green | Roche | 04887352001 |
| Critical Commercial Assays | ||
| Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit | Invitrogen | C10419 |
| Click-iT EdU Alexa Fluor 647 Imaging Kit | Invitrogen | C10340 |
| Ovation RNA-seq System V2 | NuGEN | 7102 |
| Ovation Ultralow DR Multiplex System 1–8 | NuGEN | 0330 |
| Absolutely RNA Nanoprep Kit | Agilent | 400753 |
| RNeasy Plus Micro Kit | Qiagen | 74034 |
| Foxp3/Transcription Factor Staining Buffer Set | eBioscience | 00552300 |
| Cell Stimulation Cocktail | Tonbo Biosciences | TNF-4975 |
| Ghost Dye Violet 510 Live/Dead Stain | Tonbo Bioscience | Cat# 13-0870-T100 |
| Chromium i7 Multiplex Kit | 10x Genomics | PN-120262 |
| Chromium Single Cell B Chip Kit | 10x Genomics | PN-1000073 |
| Chromium Single Cell 3’ GEM Library and Gel Bead Kit v3 | 10x Genomics | PN-1000075 |
| Deposited Data | ||
| Bulk RNA-seq data | This study | GSE126514 |
| Single cell RNA-seq data | This study | GSE140512 |
| Experimental Models: Organisms/Strains | ||
| Mouse: B6;FVB-Tg(Adipoq-cre)1Evdr/J | The Jackson Laboratory | 010803 |
| Mouse: B6.129-Tg(Adipoq-cre/Esr1*)1Evdr/J | The Jackson Laboratory | 024671 |
| Mouse: 6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J | The Jackson Laboratory | 008463 |
| Mouse: B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J | The Jackson Laboratory | 007676 |
| Mouse: B6N.129S-Pnpla2tm1Eek/J | The Jackson Laboratory | 024278 |
| Mouse: C57BL/6-Gt(ROSA)26Sortm1(HBEGF)Awai/J | The Jackson Laboratory | 007900 |
| Mouse: C57BL/6 | Charles River | 027 |
| Oligonucleotides | ||
| PCR primers, see Table S3 | This study | N/A |
| Software and Algorithms | ||
| Fiji (ImageJ) | NIH | https://fiji.sc |
| Adobe Photoshop | Adobe | https://www.adobe.com/products/photoshop.html |
| FlowJo | FlowJo, LLC | https://www.flowjo.com |
| Ingenuity Pathway Analysis | Qiagen | https://www.qiagenbioinformatics.com |
| MATLAB | MathWorks | https://www.mathworks.com |
| GraphPad Prism | GraphPad Software, Inc | https://www.graphpad.com |
| HISAT2 2.1.0 | Kim et al., 2015 | https://ccb.jhu.edu/software/hisat2/index.shtml |
| StringTie v1.3.3b | Pertea et al., 2015 | https://ccb.jhu.edu/software/stringtie/ |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Kallisto | Bray et al., 2016 | https://pachterlab.github.io/kallisto/ |
| Bustools | Melsted et al., 2019 | https://www.kallistobus.tools |
| Seurat 3.0 | Stuart et al., 2019 | https://satijalab.org/seurat/ |