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4 protocols using ki 67 b56

1

Multiparametric Flow Cytometry of Thymocytes

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Surface staining was performed for 20 minutes at room temperature and always included Fixable Viability Dye (eBioscience) for dead cell exclusion. For intracellular analysis thymocytes were fixed, permeabilized and stained using the Transcription Factor Staining Buffer Set (eBioscience), as per manufacturer’s instructions. Other anti-human mAbs used included: CD8β (SIDI8BEE), CD27 (O323), CD45RA (HI100), CD44 (IM7), CD69 (FN50), CXCR3 (1C6), Eomes (WD1928), T-bet (eBio4B10), ThPOK (ZFP-67), Runx1 (RXDMC), Runx3 (R3-5G4) and Ki67 (B56) from eBioscience/Thermo Fisher Scientific, BD Biosciences or R&D Systems. Cells were acquired in a LSRFortessa (BD Biosciences) cytometer and data was analyzed using FlowJo v10 (FlowJo, BD). For the visualization of high-dimensional data through the t-distributed stochastic neighbor embedding (t-SNE) dimensionality reduction technique, similar number of live, single cells from each condition were concatenated. tSNE parameters were set to 1,000 iterations, perplexity 30 and learning rate 4200, and based on appropriate markers.
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2

Multiparameter Flow Cytometry Analysis

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Surface and intracellular staining were performed as described previously [20 (link)]. For surface staining were used antibodies specific against mice CD3 (17A2), CD4 (RM4-5), CD8 (53–6.7), CD11a (M17/4) CD43 (1B11), CD44 (IM7), CD62L (MEL-14), CD69 (H1.2F3), CD127 (AFR134), KLRG1 (2F1), and for intracellular staining were used antibody specific against mice EOMES (Dan11mag), Foxp3 (FJK-16S), GzmB (GB11), Ki67 (B56), and T-bet (4B10) produced by eBiosciences or BioLegend. For surface staining of human cells were used antibodies specific against human CD3 (SK7), CD4 (OKT4), CD8 (HIT8a), CD45RO (UCHL1), CCR7 (G043H7), and for intracellular staining were used antibody specific against human GzmA (CB8) and GzmB (GB11) produced by BioLegend.
Data were acquired on a LSR II flow cytometer (Becton Dickinson) from 350,000–500,000 lymphocyte-gated events per sample. Analyses were done using FACSDiva software (Becton Dickinson) and FlowJo software (Treestar).
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3

Comprehensive Immune Cell Profiling

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Antibodies for cell surface staining for CD4 (RM4–5), D011.10 TCR (KJ1–26), CD25 (eBio3C7), CD44 (IM7), CD62L (MEL-14), GITR (YGITR 765), Ly6G (1A8), Ly6C (HK1.4), CD45, B220, MHC Class II (M5/114.15.2), CD11b (M1/70), CD3 (2C11), Siglec-F (E50-2440) and CD11c (N418) were purchased from eBioscience, Biolegend or BD Biosciences. Unlabeled anti-CD3 (2C11) and anti-CD28 (PV-1) were purchased from the University of California San Francisco Antibody Core. Intracellular staining for Foxp3 (FJK-16s), T-bet (4B10), IFNγ (XMG1.2), IL-17A (TC11-18H10.1), IL-10 (JES5-16E3), Ki-67 (B56) (eBioscience, Biolegend or BD Biosciences) was conducted using eBioscience Foxp3 intracellular staining reagents according to manufacturer’s instructions. Intracellular staining for phospho-STAT1 (4a) (BD Biosciences), phospho-SMAD2/3 (D27F4), phospho-AKT (D9E) and phospho-S6 Ribosomal protein (D57.2.2E) (Cell Signaling Technology) was conducted as previously described48 (link). Naïve CD4+ T cells were isolated using no-touch magnetic bead purification (MACS, Miltenyi Biotec). Where indicated, cells were further sorted as described by florescent antibody labeling using FACSAria cell sorting system (BD Biosciences). Flow cytometric analysis utilized LSRII, Canto, and FACSCalibur cytometers (BD Biosciences), and data was analyzed with FlowJo Software.
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4

Comprehensive Immune Cell Profiling

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Antibodies for cell surface staining for CD4 (RM4–5), D011.10 TCR (KJ1–26), CD25 (eBio3C7), CD44 (IM7), CD62L (MEL-14), GITR (YGITR 765), Ly6G (1A8), Ly6C (HK1.4), CD45, B220, MHC Class II (M5/114.15.2), CD11b (M1/70), CD3 (2C11), Siglec-F (E50-2440) and CD11c (N418) were purchased from eBioscience, Biolegend or BD Biosciences. Unlabeled anti-CD3 (2C11) and anti-CD28 (PV-1) were purchased from the University of California San Francisco Antibody Core. Intracellular staining for Foxp3 (FJK-16s), T-bet (4B10), IFNγ (XMG1.2), IL-17A (TC11-18H10.1), IL-10 (JES5-16E3), Ki-67 (B56) (eBioscience, Biolegend or BD Biosciences) was conducted using eBioscience Foxp3 intracellular staining reagents according to manufacturer’s instructions. Intracellular staining for phospho-STAT1 (4a) (BD Biosciences), phospho-SMAD2/3 (D27F4), phospho-AKT (D9E) and phospho-S6 Ribosomal protein (D57.2.2E) (Cell Signaling Technology) was conducted as previously described48 (link). Naïve CD4+ T cells were isolated using no-touch magnetic bead purification (MACS, Miltenyi Biotec). Where indicated, cells were further sorted as described by florescent antibody labeling using FACSAria cell sorting system (BD Biosciences). Flow cytometric analysis utilized LSRII, Canto, and FACSCalibur cytometers (BD Biosciences), and data was analyzed with FlowJo Software.
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