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7 protocols using intracellular staining permeabilization buffer

1

Mitochondrial Metabolism and Inflammation

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Macrophages were stimulated as described and incubated for 15 min in PBS containing Zombie violet dye and/ or MitoTracker Deep Red. Cells were washed, fixed with the Fixation Buffer (BioLegend) and permeabilized with the Intracellular staining permeabilization buffer (BioLegend). Mitochondrial mass was analyzed using the TOM20 antibody and the anti-rabbit Alexa488. HIF-1α and pro-IL-1β content were analyzed using APC anti-HIF-1α (R&D) and PE anti-pro-IL-1β (NJTEN3 clone, Thermo). Dead cells (Zombie violet dye positive cells) were excluded from following analysis.
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2

Multicolor Flow Cytometry Analysis

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Cells were resuspended in PBS containing 1% BSA or 2% FBS and 2 mM EDTA, and then incubated with FcR blocking reagent human (Miltenyi Biotec) or with 5% human serum at 25 °C for 5 minutes. Finally, cells were incubated with fluorochrome-conjugated antibody-mix for 20 minutes at 4°C in the dark. Cell suspension was washed with PBS 1% BSA and acquired at Navios Flow Cytometer using NAVIOS software v1.3 (Beckman Coulter), MACSQuant 10 or 16 Analyzers using MACSQuantify software v2.13 (Miltenyi Biotec). For IL-1β intracellular staining, cells were fixed and permeabilized with IC Fixation Buffer (Thermo Fisher Scientific) and intracellular staining permeabilization buffer (BioLegend) according to manufacturer’s instruction and acquired at or FACSCanto II using DIVA software v8.0.2 (BD Biosciences). Data were analyzed with FlowJo v10.6.2 (TreeStar)
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3

Flow Cytometry Analysis of Lipid Modulation on Macrophage Phenotypes and Tumor Cell Proliferation

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Flow cytometry was used to detect the effect of lipids on the characteristics of M1 or M2 macrophages and the proliferation of 4T1 cells. Briefly, after incubation of M1 and M2 macrophages with different concentrations of lipids for 48 h, cells were washed twice, detached from 24-well plates by trypsinization and resuspended in a FACS buffer containing Abs for extracellular labeling. To assess the effect of lipids on the expression of M1 or M2 macrophage markers, cells were labeled with anti-CD86 (1 μg/mL), anti-CD68 (1 μg/mL) and anti-CD163 (1 μg/mL) Abs. To assess the effect of lipids and CM+ on 4T1 cell proliferation and migration, cells were labeled with anti-E-cadherin (1 μg/mL) and anti-vimentin (1 μg/mL) Abs.
For intracellular Ab labeling, cells were first fixed in 4% paraformaldehyde (PFA) for 10 min at RT, followed by permeabilization in intracellular staining permeabilization buffer (Biolegend) for 10 min, then incubated with 100 uL intracellular staining buffer containing anti-mouse CD68-FITC Ab (1 μg/mL) or Ki-67 (1 μg/mL) on ice for 45 min. After washing with PBS, samples were resuspended in 100 μL PBA and measured by flow cytometry (BD LSR III, Bioscience). For each sample, at least 10,000 events were acquired and analyzed using FlowJo 10.1 software.
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4

Mitochondrial Metabolism and Inflammation

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Macrophages were stimulated as described and incubated for 15 min in PBS containing Zombie violet dye and/ or MitoTracker Deep Red. Cells were washed, fixed with the Fixation Buffer (BioLegend) and permeabilized with the Intracellular staining permeabilization buffer (BioLegend). Mitochondrial mass was analyzed using the TOM20 antibody and the anti-rabbit Alexa488. HIF-1α and pro-IL-1β content were analyzed using APC anti-HIF-1α (R&D) and PE anti-pro-IL-1β (NJTEN3 clone, Thermo). Dead cells (Zombie violet dye positive cells) were excluded from following analysis.
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5

Detailed Immune Cell Profiling by Flow Cytometry

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For flow cytometry experiments, the SVF suspension was isolated and blocked as mentioned above. Cells were then stained with specific cocktails of antibodies for selected clusters, Cluster 1, CD45-PECy7, CD11b-Alexa Fluor 488, CD9-APC, CD11c-PE; Cluster 2: CD45-FITC, CD11b-PE, CD206-APC, LYVE-1-PECy7; Cluster 5: CD45-FITC, CD11b-Alexa Fluor 594, Ly6a-PE, and CD34-PE/Cy7. For intracellular staining of collagen, cells were preincubated with Intracellular Staining Permeabilization Buffer (BioLegend) followed by blocking in 2.5% goat serum diluted in phosphate-buffered saline (PBS). Cells were incubated with primary rabbit anti-mouse COL1A1 antibody (Antibodies-online.com), followed by wash and secondary goat anti-rabbit antibody conjugated with Alexa Fluor 488. Finally, CD45-APC, CD11b-PE/Cy7, and Ly6a-PE were added. Data were collected by flow cytometry analyzer (BDX-20, BD Bioscience). For the in vitro study, cells were stained with CD45-APC, CD11b-AlexaFluor 488, Ly6a-PE, and sorted (Sony SY3200 “Synergy”). Antibody catalog numbers and dilutions are presented in Supplementary Table S2.
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6

Multiparametric Analysis of T-Cell Subsets

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5. -AIQ was obtained from Matrix Scientific (Columbia, SC, USA. Roswell Park Memorial Institute). RPMI 1640 medium was purchased from Sigma-Aldrich (St. Louis, MO, USA). Antibodies to FOXP3 (#SC-130666), Helios (#SC-390357), GATA3 (#SC-268), and IL-17A (#SC-374218) were purchased from Santa Cruz Biotech, (Dallas, TX, USA). GolgiStop was purchased from BD Biosciences (San Diego, CA, USA). Conjugated phycoerythrin (PE), fluoro-isothiocyanate (FITC), PE/Dazzle 594, allophycocyanin (APC). APC anti-CD4 (#100412), FITC anti-CD4 (#100510), APC anti-CXCR6 (#151106), FITC anti-CXCR6 (#151107), PE anti-FOXP3 (#126404), PE anti-Helios (#137206), APC anti-GATA3 (#653806), PE anti-IL-17A (#506903), PE anti-IL-9 (#514104), and APC anti-IL-10 (#505010) monoclonal antibodies, red blood cell lysis buffer, fixation buffer, and intracellular staining permeabilization buffer were all obtained from BioLegend (San Diego, CA, USA). TRIzol reagent was purchased from Invitrogen (Carlsbad, CA, USA). SYBR Green and High-Capacity cDNA reverse transcription kit were purchased from Applied Biosystems (Foster City, CA, USA). Primers were synthesized by GenScript (Piscataway, NJ, USA). Nitrocellulose membranes were obtained from Bio-Rad Laboratories (Hercules, CA, USA). Western blot chemiluminescence kit was purchased from Millipore (Billerica, MA, USA).
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7

Rat Acetylcholine Receptor Autoantibody Assay

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The R97-116 peptide derived from the rat (AChRα) subunit was used as an immunogen. The peptide (DGDFAIVKFTKVLLDYTGHI) was obtained from Bankpeptide Technology Co. (Hefei, China) (MW: 2252.57 Da, purity >95%). Mycobacterium tuberculosis H37RA powder was purchased from DIFCO (Franklin Lakes, NJ, USA). Freund’s adjuvants were obtained from Sigma (St. Louis, MO, USA.). Rat AChR-Ab ELISA test kits (QS41981) were purchased from Qisong Biotechnology Co. (Beijing, China). Sotrastaurin (AEB-071) was produced by GLPBIO (Montclair, CA, USA). Antibodies (anti-rat CD4-FITC, CD25-PE, and Foxp3-APC), fixation buffer, true-nuclear transcription factor buffer sets, intracellular staining permeabilization buffer, and leukocyte cell activation cocktail were purchased from Bio Legend, Inc. Erythrocyte Lysis Buffer and rat interleukin (IL)-17A-APC were purchased from eBioscience, Inc. (San Diego, CA, USA) Azathioprine (AZP) and 0.9% saline (NS) were provided by the Pharmacy Department of the 8th Medical Center of Chinese PLA General Hospital. RPMI-1640 was prepared in-house. The optical density of the test sample and the standard was determined with a Bio-Kinetics microplate reader at a wavelength of 450 nm. Flow cytometry was performed on a BD LSRII flow cytometer (BD Biosciences, Franklin Lakes, NJ, USA).
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