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22 protocols using cd45.2 104

1

Characterization of CD8+ T Cell Subsets

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Cells were incubated with αCD16/32 (clone 2.4G2; hybridoma supernatant) and plated on U-bottom 96-well plates at ≤ 3 × 106 cells/well in complete RPMI. Where indicated, cells were stained with Kb-SIINFEKL tetramer APC (NIH tetramer core) at 37°C for 30 min in the presence of αCD8α (53–6.7; Biolegend). For live-dead and surface staining, cells were washed with media, and stained in media for 20 min at RT with Fixable Viability Dye 780 (eBioscience) and surface antibodies for CD19 (6D5, Biolegend), CD8α (53–6.7, Biolegend), CD44 (IM-7; Tonbo), CD127 (A7R34, Tonbo), KLRG1 (2F1/KLRG1, Biolegend), CD45.1 (A20, Biolegend), CD45.2 (104, Biolegend), CD122 (TM-b1, Biolegend). After wash with RPMI, cells were fixed and permeabilized for 45 min at RT in Foxp3/Transcription Factor 1× Fix/Perm solution (Tonbo), followed by wash with 1× Flow Cytometry Perm Buffer (Tonbo) and intracellular staining for 45 min at RT with intracellular antibodies, including TCF1 (C63D9; Cell Signaling Technology), FOXO1 (C29H4, Cell Signaling Technology), T-bet (4B10, Biolegend), EOMES (Dan11mag; eBioscience). The cells were washed twice and resuspended in 1× Flow Cytometry Perm Buffer (Tonbo). Flow cytometry data was acquired on a four-laser (405, 488, 561, 638 nm) CytoFlex S (Beckman Coulter) and analyzed using FlowJo software (BD Biosciences).
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2

Multicolor Flow Cytometry Panel

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Antibodies were conjugated to fluorochromes (FITC, PE, PECy7, APC, APCCy7, Pacific Blue, and BV711) and were specific for the following mouse antigens: CD3 (145-2C11; Biolegend), CD11b (M1/70; Sony), CD11c (HL3; Biolegend), CD19 (6D5; Sony), CD45.2 (104; Biolegend), Ly6C (Hk1.4; eBioscience), Ly6G (RB6-8C5; BD Pharmingen), CD45 (30F11; Sony), and TER119 (Ter119; BD Pharmingen).
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3

Immunophenotyping and Mitochondrial Analysis of NK Cells

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Cell-surface staining was performed with fluorophore-conjugated antibodies against the following proteins: NK1.1 (PK136, Tonbo), CD11b (M1/70, Tonbo), CD27 (LG.3A10, BioLegend), KLRG1 (2F1, eBioscience), CD69 (H1.2F3, BioLegend), Ly49H (3D10, eBioscience), CD107a (1D4B, BioLegend), CD45.1 (A20, BioLegend), CD45.2 (104, Biolegend), TCRβ (H57–597, BioLegend), IFN-γ (XMG1.2, BioLegend), and Ly49D (4E5, BioLegend). Unless otherwise indicated, NK cells were defined as TCRβ-NK1.1+ cells. Intracellular cytokine staining was performed with the Cytofix/Cytoperm Plus Kit (BD). NK cells were enriched from spleens as mentioned above, stained with cell-surface antibodies, and then incubated with various dyes in Hank’s balanced salt solution plus Mg and Ca as follows: 100 nM Mitotracker Green (Life Technologies) for 30 min at 37°C to measure mitochondrial mass, 100 nM TMRE for 30 min at 37°C to measure mitochondrial membrane potential, 5 μm MitoSOX red (Invitrogen) for 15 min at 37°C to measure mitochondria-associated ROS, or 1:400 Cyto-ID autophagy detection reagent (Enzo Life Sciences) for 30 min at 37°C to measure autophagosomes. Flow cytometry and cell sorting were performed on the LSR II and Aria II cytometers (BD Biosciences), respectively. For experiments involving real-time PCR, cell populations were sorted to >95% purity. Data were analyzed with FlowJo software (Tree Star).
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4

Multiparameter FACS and Cell Sorting

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The following antibodies were used in fluorescence-activated cell sorting (FACS) and cell sorting: CD45.1 (A20, BioLegend), CD45.2 (104, BioLegend), CD4 (H129.19, BD Pharmingen), CD25 (7D4, BD Pharmingen), IL-17A (TC11-18H10.1, BD Pharmingen), IFN-g (XMG1.2, BD Pharmingen), CD44 (IM7, Bio-Legend), CD62L (MEL-14, BioLegend), CD25 (7D4, BD Pharmingen), Lag3 (46-2231-80, eBioscience), Nrp1 (FAB566A, R&D Systems), Ki67 (SolA15, eBioscience), CTLA4 (14D3, eBioscience), GITR (DTA-1, eBioscience), ICOS (C398.4A, BioLegend), Foxp3 (FJK-16 s, eBioscience), p27 (sc-776, Santa Cruz Biotechnology), p-p27 (ab85047, Abcam), Foxo1 (ab39670, Abcam), p-Foxo1 (9461S, Cell Signaling Technology), Raptor (ab5454, Abcam), Brdu (B44, BD Pharmingen).
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5

Multiparametric Flow Cytometry Analysis

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Cell suspensions from mouse liver, BM (one femur and tibia), spleen, thymus, mesenteric lymph nodes, and peritoneal cavity were processed as previously described (47 (link)), and data were acquired on a FACSCanto10c (BD) and analyzed with FlowJo Software (Tree Star).
The following anti-mouse antibodies were used: B220 (RA3-6B2, BioLegend), BAFFR (7H22-E16,BD), BP-1 (6C3, BioLegend), CD3e (145-2C11, eBioscience), CD4 (GK1.5, eBioscience), CD5 (53-7.3, BioLegend), CD8 (53-6.7, BioLegend), CD9 (MZ3, BioLegend), CD11b (M1/70, eBioscience), CD19 (6D5, 1D3, BioLegend), CD21/CD35 (7E9, BioLegend), CD23 (B3B4, BioLegend), CD24 (M1/69, BioLegend), CD25 (PC61, Biolgend), CD43 (S7, BioLegend), CD44 (IM7, BioLegend), CD45.1 (A20, BioLegend), CD45.2 (104, BioLegend), CD69 (H1.2F3, BioLegend), CD80 (16-10A1, BioLegend), CD86 (GL1, BioLegend), CD93 (AA4.1, BioLegend), DAPI (BIOTIUM), Gr-1 (RB6-8C5, eBioscience), IgDa (AMS-9.1, BioLegend), IgD (11-26c, BioLegend), IgMa (DS-1, MA-69, BioLegend), IgM (Il/41, RMM-1, BioLegend), TCRγδ (GL3, BioLegend), Live dead dye (Zombie Aqua Dye, BioLegend), Live dead dye (Zombie NIR, BioLegend), pERK (4B11B69, BD), pPLCγ2 (K86-1161, BD), Lin28b (AP1485C, ABGENT), and anti-rabbit IgG (BioLegend).
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6

Single-Cell Immunophenotyping Protocol

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Single cell suspensions were plated in 96-well V-bottom plates and stained at 4 °C. Dead cells were removed using LIVE/DEAD Fixable Dead Cell Stain Kit (Invitrogen). The following antibodies were used: CD3 (17A2, Biolegend), CD11b (M1/70, Biolegend), CD11c (N418, Biolegend), CD16/32 (93, Biolegend), CD34 (HM34, Ebioscience), CD36 (MF3, Bio-Rad), CD45 (30F11, Biolegend), CD45.1 (A20, Biolegend), CD45.2 (104, Biolegend), CD115 (AFS98, Biolegend), CD206 (MR5D3, BD), B220 (RA3-6B2, Biolegend), c-kit (ACK2, Biolegend), Clec12a (5D3CLEC12A, Biolegend), CXCR4, (2B11, BD), F4/80 (BM8, Biolegend), Ly-6C (HK1.4, Biolegend), Ly-6G (1A8, BD Biosciences), MHCII (M5/114.15.2, Biolegend), NK1.1 (PK136, BD Biosciences). Sca-1 (D7, Biolegend), Siglec H (551, Biolegend), TER119, (TER-119, Biolegend). Cells were acquired using a Gallios flow cytometer (Beckman Coulter) and analyzed using Kaluza software (Beckman Coulter). GFP and YFP signals in chemotherapy and adoptive transfer experiments were separated by exciting GFP using the 405-nm violet laser using the 550/40-nm emission filter.
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7

Multiparameter Flow Cytometric Analysis of Myeloid Cells

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Flow cytometry was performed as previously described. Briefly, to analyze phenotypes of peritoneal MFs, isolated cells were suspended in FACS wash buffer (2% BSA in PBS) and stained with conjugated monoclonal antibodies (FITC-, PE-, or APC). Anti-mouse monoclonal antibodies (mAb) for CD11b (M1/70), F4/80(BM8), I-Ab (AF6-120.1), CD40 (3/23), CD80 (16-10A1), Gr-1 (RB6-8C5), PD-L2 (TY25), and B220 (RA3-6B2) were purchased from Biolegend (San Diego, CA). PE-conjugated anti-PD-L1 mAb (M1H5) was purchased from eBioscience (San Diego, CA). After staining, cells were washed with FACS wash buffer and fixed with FACS Lysing Solution (BD Biosciences). Samples were analyzed on a C6 cytometer (BD bioscience). To analyze donor T cell expansion after allo-BMT, isolated spleen cells were processed as above and stained with CD4 (RM4-4), CD8a (53-6.7), CD90.2 (53-2.1), CD229.1 (30C7), CD45.1 (A20), and CD45.2 (104) mAbs purchased from Biolegend. For intracellular staining of Foxp3, cells were washed with permeabilization buffer (eBioscience) and stained with PE-conjugated anti-Foxp3 mAb (FJK-16s; eBioscience) for 30 min at 4°C. The cells were then washed with FACS wash buffer and analyzed on a C6 cytometer (BD bioscience).
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8

Multiparameter FACS and Cell Sorting

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The following antibodies were used in fluorescence-activated cell sorting (FACS) and cell sorting: CD45.1 (A20, BioLegend), CD45.2 (104, BioLegend), CD4 (H129.19, BD Pharmingen), CD25 (7D4, BD Pharmingen), IL-17A (TC11-18H10.1, BD Pharmingen), IFN-g (XMG1.2, BD Pharmingen), CD44 (IM7, Bio-Legend), CD62L (MEL-14, BioLegend), CD25 (7D4, BD Pharmingen), Lag3 (46-2231-80, eBioscience), Nrp1 (FAB566A, R&D Systems), Ki67 (SolA15, eBioscience), CTLA4 (14D3, eBioscience), GITR (DTA-1, eBioscience), ICOS (C398.4A, BioLegend), Foxp3 (FJK-16 s, eBioscience), p27 (sc-776, Santa Cruz Biotechnology), p-p27 (ab85047, Abcam), Foxo1 (ab39670, Abcam), p-Foxo1 (9461S, Cell Signaling Technology), Raptor (ab5454, Abcam), Brdu (B44, BD Pharmingen).
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9

Murine Lymphoid Tissue Dissociation

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Cell suspensions were obtained from the spleen, the PP, the MLN and the AA LN (lumbar and renal lymph nodes). Jejunum and colon sections from PBS and LCWE-injected mice were harvested and dissociated into single-cell suspensions with a gentleMACS™ Octo Dissociator (Miltenyi Biotec) and a mouse Lamina Propria Dissociation kit (Miltenyi Biotec) following the complete protocol from the manufacturer. The following antibodies against the respective murine antigens were used: IgA (mA-6E1,Thermo Fisher Scientific), CD19 (eBio1D3, Thermo Fisher Scientific), CD4 (RM4–5, Tonbo Biosciences), CD3 (145–2C11, BioLegend and Tonbo Biosciences), CD45.1 (A20, Thermo Fisher Scientific), CD45.2 (104, BioLegend), CD95 (SA367H8, BioLegend), GL-7 (GL-7, BioLegend). Dead cells were routinely excluded based on the staining of Fixable Viability dye (FVD) eFluor 506 (Thermo Fisher Scientific). Cell numbers were calculated by flow cytometry with the CountBright Absolute Counting Beads (Thermo Fisher Scientific). Stained cells were analyzed on a LSRII (BD Biosciences) and the data were processed using Flowjo (Tree Star Inc.).
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10

Multiparameter Flow Cytometry of Immune Cells

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Cells were seeded in a 96-well plate and stained with fluorochrome-conjugated antibodies for 20 min at 4 °C in the dark. Cells were subsequently washed with PBS containing 2% fetal bovine serum. The following antibodies were used: CD8 (53-6.7; BD Biosciences), CD62L (MEL-14; BD Biosciences), CCR7 (4B12; eBioscience, San Diego, CA, USA), CD103 (2E7; eBioscience), CD25 (PC61; BioLegend), CD45.2 (104; BioLegend), CD44 (IM7; BioLegend), CD69 (H1.2F3; BioLegend), and CD4 (RM4-5; BioLegend). Cells were stained with LIVE/DEAD® Fixable Blue Dead Cell Stain (Invitrogen, Carlsbad, CA, USA) to discriminate dead cells. All stained samples were acquired using CytoFLEX LX instrument (Beckman Coulter), and the data were analyzed using the FlowJo software (BD Biosciences).
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