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2 protocols using eomes

1

Western Blot Analysis of Cellular Signaling

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T cells were lysed in Ripa buffer containing a protease inhibitor and phosphatase inhibitor cocktail (Thermo Fisher Scientific, Waltham, MA, USA). Cell lysates were centrifuged at 4 °C at 12,000× g for 10 min, separated by SDS-PAGE and transferred onto a PVDF membrane. The membrane was blocked with 5% BSA in PBS containing 0.05% Tween-20 and incubated with various antibodies recognizing pAMPKα1 (T172), pAMPKα1 (S485), pS6 (S235/236), peIF4E (S209), pULK1 (S555), ATG7, AQP9, PGC1α, TFAM, OPA1, pDRP1 (S616), ID2, ID3, cMyb, cMyc, Blimp1, T-bet, ZEB2, FOXO1, TCF1, TRAF6, pTSC2 (S1387), Eomes, HIF-1α and β-actin (Cell Signaling Technology) and the Complex I subunit NDUFA9 (Abcam, Cambridge, MA, USA). The membranes were imaged using a BioRad Chemidoc MP (Bio-Rad, Hercules, CA, USA) after a second incubation step with a horseradish peroxidase-conjugated goat anti-rabbit IgG or goat anti-mouse IgG (Cell Signaling) secondary antibody [18 (link)].
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2

Isolation and Staining of Immune Cells

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Single-cell suspensions were prepared from spleen or lymph node by mechanical disruption, and intestinal tissue and tumor were processed as described previously (Milner et al., 2017 (link)). RBCs were lysed with ACK buffer (140 mM NH4Cl and 17 mM Tris-base, pH 7.4). The following antibodies were used for surface staining (all from eBioscience unless otherwise specified): CD8 (53–6.7), CD27 (LG-7F9), CD43 (eBioR2.60), CD44 (IM7), CD45.1 (A20-1.7), CD45.2 (104), CD69 (H1.2F3; BioLegend), CD103 (2E7), Tim3 (RMT3-23), CD127 (A7R34), CD62L (MEL-14), KLRG1 (2F1), PD-1 (J43), and CX3CR1 (SA011F11; BioLegend); or intracellular staining: GzB (GB12; Invitrogen), Eomes (Dan11mag), TCF1 (C63D9; Cell Signaling Technology), T-bet (4B10), and Ki-67 (SolA15). The H-2Db-GP33-41 tetramer was obtained from the National Institutes of Health Tetramer Core. Intracellular staining was performed using the Foxp3 Transcription Factor Staining Buffer Set (eBioscience). CellTrace Violet (Ebioscience) and BrdU (BD PharMingen) were used per manufacturer instructions where 2 mg BrdU was administered i.p. 2 h before tissue harvesting. For flow cytometry analysis, all data were acquired on a BD LSRFortessa X-20 or a BD LSRFortessa. Cell sorting was performed on BD FACSAria or BD FACSAria Fusion instruments.
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