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7 protocols using nfatc1

1

Signaling Pathways in Cell Activation

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The following chemicals were obtained: Cyclosporin A (TCI Chemical cat no.C2408), Bay11–7082 (Enzo cat no.E1279), PP2 (Tocris cat no.1407), Gö 6983 (Cayman Chemical cat no.13311), INCB3284 (Cayman Chemical cat no.1163). 200,000 cells seeded in 24 well plates were treated with/without inhibitors. Protein cell lysates were prepared and immunoblotted using procedures described24 (link). Membranes were blotted with antibodies to: CD154 (Santa Cruz Biotechnology cat no. sc978), NFATc1 (Biolegend, cat no.649601), phospho-IKBa (ser32) (Cell Signaling Technology cat no. 9246), IΚBα or ACTIN (Sigma, cat no.A5441).
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2

Multiparametric Immune Profiling of T Cells

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Cells were stained with CD3 (BioLegend, clone: HIT3a), CD8 (BioLegend, clone: SK1), CD45RO (BioLegend, clone: UCHL1), T-bet (BioLegend, clone: 4B10), Eomes (R&D Systems, clone: 644730), NFATC1 (BioLegend, clone: 7A6), PD-1 (BioLegend, clone: EH12.2H7), TIM-3 (BioLegend, clone: F38-2E2), CTLA4 (BioLegend, clone: L3D10), LAG3 (BioLegend, clone: 11C3C65), Bcl-XL (Abcam, clone:7B2.5), FABP5 (R&D Systems, clone: 311215),CPT1α (Proteintech, 15184-1-AP), CD137 (BioLegend, clone: 4B4-1), mito Tracker Red CMXROS (Invitrogen, M7512), TMRM (Invitrogen, M20036), LIVE/DEAD Viability/Cytotoxicity Kit (Invitrogen, L3224), CD27 (BioLegend, clone: M-T271), CD127 (eBioscience, clone: eBioRDR5), IFNγ (BD Pharmingen, clone: B27), TCF7 (BioLegend, clone: 7F11A10), IRF4 (BioLegend, clone: IRF4.3E4), Blimp1 (BD Pharmingen, clone: 6D3), BCL2 (Cell Signaling Technology, clone: 124), Ki67 (Abcam, clone: B126.1), PPARγ (Abcam, clone: EPR18516), Annexin V (BD Pharmingen, 556547), CFSE (BD Pharmingen, 565082), KLRG1 (BioLegend, clone: 2F1/KLRG1), as well as BODIPY 493/503 (Invitrogen, D3922) and BODIPY FL C16 (Invitrogen, D3821). For intracellular staining, cells were given PMA/ionomycin (BioLegend, 423303) re-stimulation and then intracellular staining was performed as previously described.6 (link) FACS analysis was performed on a BD FACS Aria II flow cytometer and analyzed by FlowJo V.6 software.
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3

Multiparametric Flow Cytometry Analysis

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The following human-specific antibodies were purchased and used for flow detection, including against CD4(PE-CY7), CD27(APC), CD19(APC-CY7), CD1d(APC), IgM(FITC), CD24(PerCP/CY5.5), CD147(PE), CD25(FITC), CD71(PE), CD73(PerCP/CY5.5), CD39(FITC), TIM-1(PE), NFAT1(PE), and NFATc1(FITC), which were purchased from BioLegend, and GSK-3β(BV421), which was purchased from BD Pharmingen. Antibodies against IL-10(PE), TGF-β(FITC), GSK-3β(BV421), NFAT1(PE), and NFATc1(FITC) were used for intracellular flow cytometry assays, while the others were used for cell surface staining. Using CATON II instrument (BD Bioscience) for sufficient sample acquisition, using FlowJo VII (TreeStar) to analyze the data.
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4

Investigating FasL-Mediated Signaling Pathways

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FasL (ALX-522-020-C005) was purchased from Enzo Life Sciences (Farmingdale, NY, USA). LY294002 and FK506 were purchased from Cell Signaling (Beverly, MA, USA) and InvivoGen (San Diego, CA, USA), respectively. DcR3 (catalogue No. 4758; 1:1000 dilution), phosphorylated Akt Serine 473 (pAkt; catalogue No. 4060/clone D9E; 1:1000 dilution), Akt (catalogue No. 9272; 1:1000 dilution), NFATc1 (catalogue No. 8032/clone D15F1; 1:1000 dilution), pan-cadherin (catalogue No. 4073/clone 28E12; 1:1000 dilution), phosphorylated GSK-3β Serine 9 (pGSK-3β; catalogue No. 5587/clone D1A3; 1:1000 dilution) and GSK-3β (catalogue No. 9315/clone 27C10; 1:1000 dilution) antibodies were purchased from Cell Signaling (Beverly, MA, USA). GAPDH (catalogue No. SC-25778/clone FL335; 1:2000 dilution) and lamin A/C (catalogue No. MABE 481/clone EP4520; 1:2000 dilution) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA) and Millipore (Bedford, MA, USA), respectively. For immunohistochemistry, DcR3 (catalog No. 333202/clone B08-35; 1:100 dilution) and NFATc1 (catalog No. 649601/clone 7A6; 1:100 dilution) antibodies were purchased from Biolegend (San Diego, CA, USA).
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5

CUT&RUN Antibody Profiling Protocol

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The following antibodies were used for CUT&RUN: Runx1 (Thermo Fisher: PA5–19638), TCF1 (Cell Signaling Technology: 2203S), Ets1 (Cell Signaling Technology: 14069), T-bet (Santa Cruz Biotechnology: sc-21003 X), IRF4 (Santa Cruz Biotechnology: sc-6059), c-Jun (Abcam: ab31419), NFATc1 (Biolegend: 649607), Bhlhe40 (Novus Biologicals: NB100–1800SS), Brg1 (Abcam: ab110641), Chd4 (Abcam: ab72418), Ruvbl1 (Proteintech group: 10210–2-AP), Snf2h (Abcam: ab3749).
The following clones of fluorescently conjugated antibodies were obtained from BD Biosciences, Biolegend, Thermo Fisher, or Tonbo Bioscience and used for flow cytometry at a 1:400 dilution: CD45 (30-F11), TCRβ (H57–597), CD4 (RM4–5), CD8a (53–6.7), CD44 (IM7), CD62L (MEL-14).
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6

CUT&RUN Antibody Profiling Protocol

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The following antibodies were used for CUT&RUN: Runx1 (Thermo Fisher: PA5–19638), TCF1 (Cell Signaling Technology: 2203S), Ets1 (Cell Signaling Technology: 14069), T-bet (Santa Cruz Biotechnology: sc-21003 X), IRF4 (Santa Cruz Biotechnology: sc-6059), c-Jun (Abcam: ab31419), NFATc1 (Biolegend: 649607), Bhlhe40 (Novus Biologicals: NB100–1800SS), Brg1 (Abcam: ab110641), Chd4 (Abcam: ab72418), Ruvbl1 (Proteintech group: 10210–2-AP), Snf2h (Abcam: ab3749).
The following clones of fluorescently conjugated antibodies were obtained from BD Biosciences, Biolegend, Thermo Fisher, or Tonbo Bioscience and used for flow cytometry at a 1:400 dilution: CD45 (30-F11), TCRβ (H57–597), CD4 (RM4–5), CD8a (53–6.7), CD44 (IM7), CD62L (MEL-14).
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7

Signaling Pathways in Cell Activation

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The following chemicals were obtained: Cyclosporin A (TCI Chemical cat no.C2408), Bay11–7082 (Enzo cat no.E1279), PP2 (Tocris cat no.1407), Gö 6983 (Cayman Chemical cat no.13311), INCB3284 (Cayman Chemical cat no.1163). 200,000 cells seeded in 24 well plates were treated with/without inhibitors. Protein cell lysates were prepared and immunoblotted using procedures described24 (link). Membranes were blotted with antibodies to: CD154 (Santa Cruz Biotechnology cat no. sc978), NFATc1 (Biolegend, cat no.649601), phospho-IKBa (ser32) (Cell Signaling Technology cat no. 9246), IΚBα or ACTIN (Sigma, cat no.A5441).
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