| Antibody |
Anti-PDGFRalpha antibody (goat polyclonal) |
R&D Systems |
Mouse PDGFRalpha antibody; cat no. AF1062 |
Diluted 1:70 in blocking buffer. |
| Antibody |
Anti-GPNMB antibody (goat polyclonal) |
R&D Systems |
Mouse osteoactivin/GPNMB antibody; cat no. AF2330 |
Dilute 1:400 in blocking buffer. |
| Antibody |
Anti-MHCII antibody (rat monoclonal) |
Biolegend |
Alexa Fluor 647 rat anti-mouse I-A/I-E antibody; cat no. 107617 |
Diluted 1:100 in blocking buffer. |
| Antibody |
Anti-MKI67 antibody (rabbit monoclonal) |
Invitrogen |
Ki-67 recombinant rabbit monoclonal antibody; cat no. MAS-14520 |
Diluted 1:125 in blocking buffer. |
| Antibody |
Anti-PLIN1 antibody (goat polyclonal) |
Everest Biotech |
Goat anti-perilipin 1 (C terminus) antibody; cat no. EB07728 |
Diluted 1:200 in blocking buffer. |
| Antibody |
Anti-F4/80 antibody (rat monoclonal) |
Bio-Rad |
rat anti mouse F4/80 antibody; cat no. MCA497GA |
Diluted 1:125 in blocking buffer. |
| Antibody |
Anti-NNAT antibody (rabbit polyclonal) |
Abcam |
Anti-Neuronatin antibody; ab27266 |
Diluted 1:400 in blocking buffer. |
| Antibody |
Anti-IgG Alexa Fluor 647 (donkey polyclonal) |
Abcam |
Donkey anti-rat secondary antibody; cat no. ab150155 |
Diluted 1:250 in blocking buffer. |
| Antibody |
Anti-IgG Alexa Fluor 568 (donkey polyclonal) |
Invitrogen |
Donkey anti-goat secondary antibody; cat no. A11057 |
Diluted 1:250 in blocking buffer. |
| Antibody |
Anti-IgG Alexa Fluor 488 (donkey polyclonal) |
Invitrogen |
Donkey anti-goat secondary antibody; cat no. A11055 |
Diluted 1:250 in blocking buffer. |
| Antibody |
Anti-IgG Alexa Fluor 647 (donkey polyclonal) |
Invitrogen |
Donkey anti-goat secondary antibody; cat no. A21447 |
Diluted 1:250 in blocking buffer. |
| Antibody |
Anti-IgG Alexa Fluor 594 (donkey polyclonal) |
Invitrogen |
Donkey anti-rabbit secondary antibody; cat no. A21207 |
Diluted 1:250 in blocking buffer. |
| Antibody |
Anti-IgG Alexa Fluor 594 (goat polyclonal) |
Invitrogen |
Goat anti-rat secondary antibody; cat no. A11007 |
Diluted 1:250 in blocking buffer. |
| Chemical compound, drug |
EdU |
Invitrogen |
5-Ethynyl-2‘-deoxyuridine; cat no. A10044 |
Diluted in sterile PBS. |
| Chemical compound, drug |
Tamoxifen |
Cayman Chemical |
Tamoxifen; cat no. 13258 |
Diluted in corn oil. |
| Chemical compound, drug |
CL316,243 |
Sigma-Aldrich |
C5976 |
|
| Chemical compound, drug |
Paraformaldehyde (PFA) |
Electron Microscopy Sciences |
Paraformaldehyde 16% Solution, EM Grade; cat no. 15710 |
Dilute to 4% PFA in PBS. |
| Chemical compound, drug |
Sucrose |
Fisher Scientific |
D-Sucrose; cat no. BP220-1 |
|
| Chemical compound, drug |
O.C.T Compound |
Fisher Heathcare |
Tissue Plus O.C.T. Compound Clear; cat no. 23-730-572 |
|
| Chemical compound, drug |
Triton X-100 |
Sigma |
Triton X-100 laboratory grade; cat no. X100-500ML |
|
| Chemical compound, drug |
ProLong Gold antifade reagent |
Invitrogen |
ProLong Gold antifade reagent; cat no. P36930
|
Coverslip mounting media |
| Chemical compound, drug |
Collagenase Type 2 |
Worthington Biochemical Corporation |
Collagenase Type 2; cat no. LS004177
|
Tissue digestion reagent |
| Chemical compound, drug |
HBSS |
Sigma-Aldrich |
Hanks' Balanced Salt Solution; cat no. H1387−10 × 1 L |
Tissue digestion reagent |
| Chemical compound, drug |
HEPES |
Sigma-Aldrich |
cat no. H4034 |
Tissue digestion reagent; FACs Buffer |
| Chemical compound, drug |
Sodium Bicarbonate |
Fisher Scientific |
Sodium Bicarbonate (Powder/Certified ACS); cat no. S233-500 |
Tissue digestion reagent; RBC lysis buffer |
| Chemical compound, drug |
FF-BSA |
Gemini Bio-products |
Bovine Serum Albumin, Fatty Acid Free; cat no. 700–107 P |
Tissue digestion reagent |
| Chemical compound, drug |
EDTA |
Millipore Sigma |
Ethylenediaminetetraacetic acid (EDTA), Tetrasodium Tetrahydrate Salt; cat no. 13235-36-4 |
Tissue digestion reagent; FACs Buffer |
| Chemical compound, drug |
FBS |
Atlanta Biologicals |
Fetal Bovine Serum, Heat-inactivated; S11550H |
FACs Buffer |
| Chemical compound, drug |
Ammonium Chloride |
Fisher Scientific |
Ammonium Chloride (Crystalline/Certified ACS); cat no. A661-500 |
RBC lysis buffer |
| Chemical compound, drug |
TRIzol |
Ambion by Life Technologies |
TRIzol Reagent; cat no. 15596018 |
|
| Chemical compound, drug |
Dextran sulfate |
Sigma-Aldrich |
cat no. D8906 |
|
| Commercial assay or kit |
Click-iT EdU Cell Proliferation Kit for Imaging, Alexa Fluor 488 dye |
Invitrogen |
cat no. C10337
|
|
| Commercial assay or kit |
Debris Removal Solution |
Miltenyi Biotec |
cat no. 130-109-398 |
|
| Commercial assay or kit |
Lineage Cell Depletion Kit |
Miltenyi Biotec |
Lineage Cell Depletion Kit, mouse; cat no. 130-090-858 |
|
| Commercial assay or kit |
Chromium Single Cell 3’ Library & Gel Bead Kit v2 |
10X Genomics |
cat no. 120237 |
|
| Commercial assay or kit |
Chromium Single Cell 3’ Library & Gel Bead Kit v3 |
10X Genomics |
cat no. 1000092 |
|
| Commercial assay or kit |
Chromium Single Cell A Chip Kit |
10X Genomics |
cat no. 120236 |
|
| Commercial assay or kit |
Chromium i7 Multiplex Kit |
10X Genomics |
cat no. 120262 |
|
| Commercial assay or kit |
Bioanalyzer High Sensitivity DNA kit |
Agilent Biotechnologies |
2,100 Bioanalyzer High Sensitivity DNA kit; cat no. 5067–4626 |
|
| Commercial assay or kit |
Direct-zol RNA Miniprep Kit |
Zymo Research |
cat no. R2050 |
|
| Commercial assay or kit |
High Sensitivity D1000 ScreenTape for DNA Analysis |
Agilent Biotechnologies |
cat no. NC1786959 |
|
| Commercial assay or kit |
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina |
Lexogen |
cat no. 113.96 |
|
| Commercial assay or kit |
KAPA SYBR Fast Universal qPCR Kit – Illumina Kapa |
Kapa Biosystems |
cat no. 07960441001 |
|
| Commercial assay or kit |
High Capacity cDNA Reverse Transcription Kit |
Applied biosystems |
cat no. 4368814 |
|
| Commercial assay or kit |
DyNAmo HS SYBR Green qPCR Kit |
Thermoscientific |
cat no. F-410XL |
|
| Commercial assay or kit |
TrueVIEW |
Vector Laboratories |
cat no. SP-8400 |
|
| Other |
Micro-osmotic Pump |
ALZET |
Micro-osmotic Pump, 0.5 uL/hr; cat no. 1007D |
Experimental model and subject details; continuous CL infusion |
| Other |
Normal Donkey Serum |
Fisher |
Jackson Immunoresearch SERUM NORMAL DONKEY; cat no. 017-000-121 |
Tissue processing and immunohistochemistry; blocking buffer |
| Other |
Normal Goat Serum |
Sigma |
cat no. G-9023 |
Tissue processing and immunohistochemistry; blocking buffer |
| Other |
Lens Culinaris Agglutinin (LCA) DyLight 649 |
Vector Laboratories |
DL-1048 |
Diluted 1:150 in blocking buffer. |
| Other |
HCS LipidTOX Deep Red neutral lipid stain |
Invitrogen |
cat no. H34477
|
Diluted 1:500. |
| Other |
DAPI |
Sigma |
D9542 |
20 mg/mL; dilute 1:2,000 |
| Other |
100 µm Sterile Cell Strainer |
fisherbrand |
Sterile Cell Strainer 100 µm; cat no. 22-363-549 |
Isolation of stromal vascular cells for mouse iBAT single cell |
| Other |
40 µm Sterile Cell Strainer |
fisherbrand |
Sterile Cell Strainer 40 µm; cat no. 22-363-547 |
Isolation of stromal vascular cells for mouse iBAT single cell |
| Other |
MS Columns |
Miltenyi Biotec |
cat no. 130-042-201 |
Magnetic bead enrichment of cellular subtypes |
| Other |
OctoMACS Separator |
Miltenyi Biotec |
cat no. 130-042-109 |
Magnetic bead enrichment of cellular subtypes |
| Other |
Chromium Controller Instrument |
10X Genomics |
cat no. 1000204 |
Single-cell RNA library preparation and sequencing |
| Other |
Bst LF polymerase |
New England Biolabs |
cat no. M0275L |
Single-molecule fluorescence in situ hybridization (smFISH) |
| Other |
Digest-All 3 |
ThermoFisher |
cat no. 003009 |
Single-molecule fluorescence in situ hybridization (smFISH) |
| Software, algorithm |
Cell Ranger v3.0.1 |
10X Genomics |
|
|
| Software, algorithm |
SoupX v1.0.1 |
PMID:33367645
|
|
|
| Software, algorithm |
Seurat v3.1.5 |
PMID:31178118
|
|
|
| Software, algorithm |
CellPhoneDB v2.1.3 |
PMID:32103204
|
|
|
| Software, algorithm |
NicheNet v0.1.0 |
PMID:31819264
|
|
|
| Software, algorithm |
CASAVA v1.8.2 |
Illumina |
|
|
| Software, algorithm |
STAR-2.6.1d |
PMID:23104886
|
|
|
| Software, algorithm |
Htseq v0.11.2 |
PMID:25260700
|
|
|
| Software, algorithm |
iDEP v0.95 |
PMID:30567491
|
|
|
| Software, algorithm |
GraphPad Prism v9.3.1 |
GraphPad Software |
|
|
| Software, algorithm |
Imaris Viewer x64 v9.9.0 |
Oxford Instruments Group |
|
|
| Strain, strain background (Mus musculus) |
C57 |
Jackson Labs |
C57BL/6J; stock no. 000664 |
|
| Strain, strain background (Mus musculus) |
LSL-tdTomato |
Jackson Labs |
B6.Cg-Gt(ROSA)26Sor_tm9(CAG-tdTomato)Hze/J; stock no. 007909 |
|
| Strain, strain background (Mus musculus) |
Pdgfra-CreERT2
|
Jackson Labs |
B6.129S-Pdgfratm1.1(cre/ERT2)Blh/J; stock no. 032770 |
|
| Strain, strain background (Mus musculus) |
Adrb1fl/fl
|
PMID:27548523
|
|
Dr. Jeffery Zigman, The University of Texas Southwestern Medical Center |
