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11 protocols using anti ha h6908

1

Immunoprecipitation and Immunoblotting Protocol

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Cells were washed with ice-cold PBS and lysed on ice for 30 min in RIPA lysis buffer (150 mM NaCl, 5% Glycerin, 1% Triton X-100, 50 mM Tris-HCl, pH7.5). For each immunoprecipitation reaction, 0.2 ml of the cell lysate was incubated with 1 μg of antibody (anti-Myc, 9E10, Santa Cruz, sc-40; anti-HA, H6908, Sigma-Aldrich) at 4 °C for 4 h, and then incubated with 10 μl of protein A/G agarose beads at 4 °C for 1 h. The sediments were then subjected to SDS-PAGE and immunoblot analysis. The antibodies used in immunoblotting were as follows: anti-Myc (9E10, Santa Cruz,1:2000), anti-HA (H6908, Sigma-Aldrich, 1:2000), anti-Flag (F3165, Sigma-Aldrich, 1:15000), anti-LC3B (ab192890, Abcam,1:1000), anti-IFITM3 (11714-1-AP, Proteintech,1:5000), anti-STAT1 (14994T, Cell Signaling Technology, 1:1000), anti-pSTAT1 (Tyr701) (7649T, Cell Signaling Technology, 1:1000), anti-FOXP3 (14-7979-82, eBioscience, 1:3000), anti-FOXO1 (2880T, Cell Signaling Technology, 1:1000), anti-Phospho-FoxO1 (Thr24)/FoxO3a (Thr32) (9464T, Cell Signaling Technology, 1:1000), anti-AKT (60203-2-Ig, Proteintech, 1:5000), anti-p-AKT (9271T, Cell Signaling Technology, 1:1000), anti-GAPDH (60004-1-Ig, Proteintech, 1:8000), anti-β-Actin (66009-1-1g, Proteintech, 1:8000), anti-LaminB (66095-1-Ig, Proteintech, 1:8000).
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2

Co-immunoprecipitation and Ubiquitination Assays

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For co-immunoprecipitation (Co-IP) assays, HEK293T cells were transfected with Myc-SNAI2 and/or HA-DEAR1 plasmids in a 6 cm plate using Mirus TransIT-LT1 transfection reagent (Mirus, MIR 2300) for 24 h. Cells were treated with MG-132 proteasome inhibitor (Calbiochem, 133407-82-6) for 2 h, before harvest. Cells were lysed with M-PER lysis buffer (ThermoFisher Scientific, 78501) and incubated with pull-down antibody overnight at 4 °C. Then, lysates were incubated with protein A/G agarose beads (Santa Cruz, sc-2003) for 2 h at 4 °C followed by three 5-min washes with RIPA lysis buffer. Proteins were eluted from beads in 30 µL of 2× SDS sample buffer for western blot analysis. Rabbit polyclonal anti-HA (H6908) or anti-Myc (M4439) from Sigma were used for pull-down and Mouse monoclonal anti-HA (H3663) from Sigma or anti-Myc (#562) from MBL International Corporation were used for immunoblotting. For in vivo ubiquitination assays, HEK293T cells were transfected with Myc-SNAI2, 8x-HA-Ub, and/or DEAR1 plasmids in a 10 cm plate. At 20 h after transfection, cells were treated with MG132 20 μmol/L for 4 h and harvested. Cells were lysed with 1× SDS-lysis buffer, denatured by heating at 95 °C for 10 min and then diluted with 0.5% NP-40 buffer and used for further analysis.
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3

Meiotic Progression and Protein Visualization

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To analyze meiotic progression, mating cells were fixed at various time points by adding formaldehyde (final concentration 4%) and Triton X-100 (final concentration 0.5%) to a 5-ml culture sample. After 30 min at room temperature, cells were pelleted and resuspended in a solution of 4% paraformaldehyde and 3.4% sucrose. The cell suspension was spread onto a slide and air dried. Slides were then washed twice with 1× phosphate-buffered saline (PBS) and once with 1× PBS containing 0.05% Triton X-100 (PBST). Cell preparations were stained with 4′,6′-diamidino-2-phenylindole (DAPI) in Vectashield (Vector Laboratories, Burlingame, CA). The same fixation method was used to visualize tagged proteins. After washing with PBST, primary antibody (anti-HA, H6908; Sigma-Aldrich, St. Louis, MO; anti-Rad51 MS-988; NeoMarkers, Fremont, CA; anti-GFP, mouse monoclonal; Takara Bio, Mountain View, CA; anti-mCherry, rabbit polyclonal; Takara Bio) was applied and incubated under a coverslip for 1–2 h. Slides were then washed, and a secondary fluorophore-coupled antibody was applied for 1 h, followed by washing and DAPI staining.
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4

Immunofluorescence Microscopy of Hematopoietic Cells

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5 × 105 cells were adhered to microscope slides using a Cytospin cytocentrifuge (Thermo Fisher Scientific) for 3 min at 200g and fixed in 4% formaldehyde (Pierce) for 15 min. Cells were permeabilised in 0.1% Triton X-100 and nonspecific staining was prevented by incubation in 3% bovine serum albumin. Antibodies were applied for 1 h at room temperature before washing, anti-HA (H6908; Sigma-Aldrich) at 1:200, anti-EVI1 (2593; Cell Signalling Technology) at 1:200, anti-RUNX1 (C-terminal, sc-28679 H-65; Santa Cruz Biotechnology) at 1:200 or anti-CBFβ (sc-56751; Santa Cruz Biotechnology), and secondary Alexa Fluor 488–conjugated anti-rabbit (Jackson ImmunoResearch) at 1:200. Slides were mounted with ProLong Gold antifade reagent with DAPI (Invitrogen). Slides were visualised using a Zeiss LSM 780 equipped with a Quasar spectral (GaAsP) detection system, using a Plan Achromat 40× 1.2 NA water immersion objective, Lasos 30 mW Diode 405 nm, Lasos 25 mW LGN30001 Argon 488, and Lasos 2 mW HeNe 594 nm laser lines. Images were acquired using Zen black version 2.1. Post-acquisition brightness and contrast adjustment was performed uniformly across the entire image.
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5

SUMOylation Protein Interaction Assay

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Anti-HA (H6908, 1:3000), anti-Flag agarose (A2220) and N-ethylmaleimide (NEM; E3876, 20 mM) were purchased from Sigma-Aldrich. Anti-SUMO1 (4940, 1:1000), anti-SAE1 (13585, 1:1000), anti-SAE2 (8688,1:1000) and anti-GAPDH (2118, 1:5000) were purchased from Cell Signaling Technology. Mouse anti-CFL1 (66057-1-Ig, 1:1000), rabbit anti-CFL1 (10960-1-AP, 1:1000), anti-GST (66001-2-Ig, 1:3000) and anti-His (66005-1-Ig, 1:1000) were purchased from Proteintech. Anti-Ubc9 (ab33044, 1:1000) and anti-SENP1 (ab108981, 1:1000) were purchased from Abcam. Anti-HA agarose (26181) and protein A/G agarose (20422) were purchased from Pierce. Protease inhibitor cocktail (B14001) was purchased from Bimake.
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6

AMPK Signaling Pathway Modulation

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LPS O111:B4 (L2630), Doxycycline (D3447), 2-Deoxy-D-glucose (D8375) and compound C (P5499) were obtained from Sigma-Aldrich. Subcellular protein fractionation kit (78840) was obtained from Thermo Fisher. Metformin (S1950) and AICAR (S1802) were obtained from Selleck Chemicals. ATP (tlrl-atpl) was obtained from InvivoGen. StrataClean resin (400714) and chemical competent cells (200315) were obtained from Agilent.
For immunoblot, AMPKα1(#2795), AMPKα2 (#2757), AMPKα1/2 (#5831) and pT172-AMPK (#2535) were purchased from Cell Signaling Technology. Anti-Flag (F1804), anti-Flag (F7425) and anti-HA (H6908) were obtained from Sigma-Aldrich. Anti-GSDMD (ab219800) and anti-Caspase-1 (ab108362) were obtained from Abcam. Anti-β-Actin (sc-47778), anti-GST (sc-138) and anti-Na/K-ATPase α1 (sc-21712) were purchased from Santa Cruz Biotechnology. Anti-IL18 (A1115) was obtained from Abclonal Technology. phospho-GSDMD S46 was generated by Abclonal Technology.
For FCAS analysis, CD45-APC-Cy7(clone 30-F11), CD3-FITC (clone 145-2C11), CD8-PerCP-Cy5.5 (clone 53-6.7) and CD4-APC (clone RM4-5) were obtained from BioLegend.
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7

Antibody Validation and Autophagy Modulation

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Anti-Flag (F3165) and anti-HA (H6908) antibodies were purchased from Sigma-Aldrich (St. Louis, MO, USA). Anti-Myc (sc40), anti-GAPDH (sc47724), anti-BECN1 (sc48341), and anti-Ub (sc-8017) antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Anti-TRAF6 (8028S) and anti-LC3 (2775S) were purchased from Cell Signaling Technology (Danvers, MA, USA). Anti-Mouse IgG H&L (HRP) (ab6728) was purchased from Abcam (Cambridge, MA, USA). Goat anti-Rabbit IgG antibody (HRP) (GTX213110-01) was purchased from GeneTex Inc. (Irvine, CA, USA). Lipopolysaccharide (LPS; L3024), dimethyl sulfoxide (DMSO; 472301), paraformaldehyde (P6148), Triton X-100 (T8787), 3-methyladenine (3-MA; M9281), and Dulbecco’s phosphate-buffered saline (DPBS; D8537) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Polyinosinic-polycytidylic acid (Poly(I:C), tlrl-pic) was purchased from InvivoGen (San Diego, CA, USA). Anti-β-arrestin 2 antibody (PA1-732) and Lipofectamine 2000 (11668019) were purchased from Thermo Fisher Scientific (Waltham, MA, USA).
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8

Antibody Sources for Signaling Pathway Analysis

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Antibodies were obtained from the following sources: Antibodies against phospho-p65 (CST-3033), p65 (CST-6956), phospho-IKKα/β (CST-2697), IKKα (CST-2682), IKKβ (CST-8943), phospho-Akt (CST-4508), Akt1 (CST-2938), Akt2 (CST-3063), phospho-S6K (CST-9205), mTOR (CST-2972), cleaved caspase 3 (CST-9664), and GAPDH (CST-5174), are purchased from Cell Signaling. Anti-Raptor ((A300-506A) and anti-Rictor (A300-458A) are from Bethyl. Anti-HA (H6908) is from Sigma. Anti-S6K (SC-8418), C-Myc (SC-40), and EGFR (SC-03) are from Santa Cruz Biotechnology. HRP-labeled anti-mouse and anti-rabbit secondary antibodies were also from Santa Cruz Biotechnology.
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9

Yeast Protein Extraction and Immunoprecipitation

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Extracts were prepared from yeast cells grown to logarithmic phase at 30°C in YPD medium. IP experiments were done with anti-HA (A2095; Sigma Aldrich) and anti-Myc (A7470; Sigma Aldrich) agarose antibodies following the procedure as described (Mishra et al., 2011 (link), 2018 (link)). Total proteins were extracted with the trichloroacetic acid (TCA) procedure (Kastenmayer et al., 2005 (link)) and quantified using the Bio-Rad DC protein quantitation assay (Bio-Rad Laboratories, Hercules, CA). Protein samples for Western blotting were size separated on SDS–polyacrylamide gels and transferred to a 0.45-µm nitrocellulose membrane. Primary antibodies used were anti-Myc (a-14, sc-789; Santa Cruz Biotechnology), anti-HA (H6908; Sigma Aldrich), and anti-Tub2 (Au et al., 2008 (link); Mishra et al., 2016 (link)). Secondary antibodies were horseradish peroxidase (HRP)-conjugated sheep anti-mouse immunoglobulin G (IgG) (NA931V) and HRP-conjugated sheep anti-rabbit IgG (NA934V), both obtained from Amersham Biosciences.
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10

Antibody Validation for Cell Signaling

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The following antibodies were used in this study: anti-Flag (M2, Sigma-Aldrich), anti-HA (H6908, Sigma-Aldrich), anti-RIPK3 (ADI-905–242, Enzo), anti-RIPK1 (38/RIP, BD), anti-MLKL (AP14272b, Abgent), anti–p-MLKL(S345, Abcam), anti–p-RIPK3 (18 (link)), anti- β-actin (AC-74, Sigma-Aldrich), and anti-ERK2 (C-14, Santa Cruz Biotechnology).
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