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2 protocols using anti bcl6 antibody

1

Isolation and Analysis of Cellular Fractions

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Nuclear and cytoplasmic extracts from naive T cells cultured for 3 days were prepared with NE-PER Nuclear and Cytoplasmic Extraction Reagents (Pierce), as previously described21 (link). The purity of the nuclear and cytoplasmic fractions was verified by probing with antibodies against Lamin B1 (D4Q4Z; 1,000×; Cell Signaling Technology). Whole-cell extracts were immunoprecipitated with an anti-Raptor (24C12; 100×; Cell Signaling Technology), anti-Def6 (Rabbit polyclonal; 100×21 (link)), anti-p62 (H-290; 50×; Santa Cruz), anti-TRAF6 (H274; 50×; Santa Cruz), or anti-HA (3F10; 50×; Roche Applied Science) antibodies. Antibodies to p-STAT3 (Y705; 1,000×), p-4E-BP (T37/46; 1,000×), 4E-BP (1,000×), p-S6K1 (S371; 1,000×), S6K1 (1,000×), p-AKT (S473; 1,000×), AKT (1,000×), p-AKT (T308; 1,000×), p-PRAS40 (T246; 1,000×), PRAS-40 (1,000×), p-AMPK (T172; 1,000×), AMPK (1,000×), p-Raptor (S792; 1,000×) and p62 (5114; 1,000×) were obtained from Cell Signaling Technology. Antibodies to IRF4 (M-17; 1,000×), TRAF6 (H274; 500×), and c-Myc (9E10; 500×) were obtained from Santa Cruz. Anti-Bcl6 antibody was obtained from BD (K112-91; 1,000×). Anti-Flag monoclonal antibody M2 (horseradish peroxidase (HRP)) was obtained from Sigma (1,000×).
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2

Immunohistochemical Analysis of Lymphoid Tissues

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Draining LNs and spleens were harvested and fixed with PLP buffer (0.05 M phosphate buffer containing 0.1 M l-lysine, pH 7.4, 2 mg/ml NaIO4, and 10 mg/ml paraformaldehyde) for 12 h. After fixation, tissues were incubated in 30% sucrose for 6 h before embedding in optimum cutting temperature compound (Tissue-Tek). 30-μm sections were cut on a cryostat (CM3050S; Leica) and adhered to slides (Super Frost Plus Gold; Electron Microscopy Services). Frozen sections were permeabilized and blocked for 1–2 h in PBS containing 0.3% Triton X-100 (Sigma-Aldrich), 1% normal mouse serum, 1% BSA, and 10% normal goat serum. Sections were stained with directly conjugated antibodies for a minimum of 5 h at room temperature or 12 h at 4°C in a humidity chamber in the dark. Anti–mouse CD80, CD86, CD45.1, CD4, and B220 antibodies were purchased from BioLegends. Anti–mouse CD11c antibody was purchased from Thermo Fisher. Anti-Bcl6 antibody was purchased from BD Biosciences. Cell nuclei were visualized with JOJO-1 (Thermo Fisher). Stained slides were mounted with Fluoromount G (eBioscience) and sealed with a glass coverslip. Each section was visually inspected by epifluorescent light microscopy, and several representative sections from different lymphoid organs were acquired using a confocal microscope (SP8; Leica) and 40× objective (numerical aperture 1.3).
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