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25 protocols using anti phospho ikkα β

1

Western Blot Analysis of Phosphorylated Proteins

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Cells were dissociated with PBS + 3 mmol/L ethylenediamine-tetraacetic acid and lysed in a buffer containing 50 mmol/L Tris, 150 mmol/L NaCl, 5 mmol/L ethylenediaminetetraacetic acid, 1% Triton X-100 (all from Sigma), and protease inhibitors (Thermo Fisher Scientific). Protein concentrations were determined using a Bio-Rad protein assay (Bio-Rad) with BSA as the standard. Samples were denatured in Laemmli buffer (Bio-Rad) with βME (2-mer-captoethanol, Bio-Rad) at 95°C for 5 minutes. Cell lysates (5 μg/lane) were run on a 10% SDS polyacrylamide gel and transferred to nitrocellulose membranes (Bio-Rad). Membranes were blocked with 5% BSA (for phosphorylated proteins) or 5% milk in Tris-buffered saline + 0.1% Tween-20 (all from Sigma) and then probed with either anti–phospho-IKKα/β (Cell Signaling Technology), anti-IKKα (Cell Signaling Technology), or anti-HA (Bethyl Laboratories, Inc.). Anti-rabbit IgG, HRP-linked or anti-mouse IgG, HRP-linked was used as secondary antibody (Cell Signaling Technology). GAPDH or β-actin (Santa Cruz Biotechnology) was used as a housekeeping gene. Blots were developed using SuperSignal West Dura Extended Duration Substrate (Thermo Fisher Scientific) and exposed to GeneMate Blue Basic Autoradiography Film (BioExpress).
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2

Characterization of Cellular Response to TNF-α

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HEK293T cells (ATCC, CRL-3216™). A549 cells (SCSP-503) and THP-1 cells (TCHu 57) were purchased from the National Collection of Authenticated Cell Cultures (Shanghai, China). Sendai virus (SeV) was kindly provided by Prof. Yanyi Wang (Wuhan Institute of Virology, CAS) and propagated in SPF chicken embryonated eggs. Lipo293™ Transfection Reagent (Beyotime Biotechnology, C0521), Lipofectamine 2000 (Invitrogen, 11,668,019), dual-specific luciferase assay kits (Promega, E1980), human recombinant TNFα (R&D Systems, 210-TA-020/CF), BAY 11–7082 (MCE, HY-13,453), mouse anti-Flag (Sigma, F3165), rabbit anti-Flag (Proteintech, 20,543–1-AP), anti-β-actin (Cell Signaling Technology, # 3700S), anti-GAPDH (HuaBio, #R1210–1), anti-LMNB1(Proteintech, 2987–1-AP), anti-HA (Origene, TA100012), anti-TNF-α (Proteintech, 60,291–1-Ig), anti-phospho-NF-κB p65(Cell Signaling Technology, #3033S), anti-phospho-IκBα (Cell Signaling Technology, #9246S), anti-phospho-IKKα/β (Cell Signaling Technology, # 2697S), anti-IKK-β (Proteintech, 15,649–1-AP) anti-IκBα (Santa Cruz, sc-1643), anti-p65 (Santa Cruz, sc-8008), donkey anti-mouse IgG-Cy3 (Absin, abs20015) and goat anti-Rabbit IgG-FITC (Absin, abs20004ss) were purchased from the indicated companies.
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3

Inflammasome Activation Pathway Assay

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Anti-IL-1β, Anti-Caspase1, TNF-α were purchased from R&D Systems (Minneapolis, MN, USA); Anti-cleaved caspase1, Anti-NLRP3, Anti-IκBα, Anti-phospho-P38, Anti-phospho-ERK, Anti-phospho-JNK, Anti-phospho-IKKα/β, and Anti-Tublin were purchased from Cell Signaling Technology (Boston, MA, USA); Anti-TAK1, Anti-phospho-TAK1, Anti-ASC and recombinant active caspase1 protein were purchased from Abcam (Shanghai, China). The ultrapure LPS and Nigericin were obtained from Sigma-Aldrich (St. Louis, MO, USA). The caspase1 activity assay kit was purchased from Beyotime Biotechnology (Shanghai, China). The Human IL-1β ELISA Kit was purchased from Boster Biological Technology (Wuhan, China).
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4

Comprehensive Western Blot Antibody Panel

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Primary antibody: anti-β-actin (sc-47778, 1:1000), anti-HA (sc-7392, 1:1000) and anti-GFAP (sc-33673, 1:200) were obtained from Santa Cruz Biotechnology (Dallas, TX, USA); Anti-iNOS (18,985–1-AP, 1:500) was purchased from Proteintech Group (Wuhan, China); anti-CD16/32 (AF1460, 1:500) was purchased from R&D systems (Minneapolis, MN, USA); anti-NF-κB p65 (#8242, 1:1000), anti-IKKα (#11,930, 1:1000), anti-Phospho-NF-κB p65 (#3033, 1:1000), anti-Phospho-IKKα/β (#2697, 1:1000), anti-Phospho-IκBα (#2859, 1:1000), anti-IκBα (#4814, 1:1000), anti-NBR1(#9891, 1:1000), anti-cleaved PARP (5625, 1:1000), anti-cleaved caspase-3 (9664, 1:1000) and anti-cleaved caspase-9 (#20,750, 1:1000) were obtained from Cell Signaling Technology (Danvers, MA, USA); anti-SENP6 (HPA024376, 1:1000) were purchased from Sigma–Aldrich (St. Louis, MO, USA); anti-Iba1 (ab283319, 1:100) was obtained from Abcam (Boston, MA, USA) and anti-NeuN (MAB377, 1:200) was purchased from Millipore Biotechnology (Schwalbach, Germany). Protein A + G agarose beads were obtained from Beyotime Biotechnology (Shanghai, China), and Ni2+-NTA agarose was purchased from QIAGEN (Dusseldorf, Germany). CHX was obtained from Calbiochem (508,739; Darmstadt, Germany).
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5

Elucidating TNF-α Signaling Pathways

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Minimal essential medium-alpha (α-MEM), fetal bovine serum (FBS), and TRIzol were purchased from Invitrogen (Carlsbad, CA). Hybond C membrane and ECL Western blotting detection system were from Amersham Biosciences (Buckinghamshire, UK). Recombinant human TNF-α and the anti-TNFR1 neutralizing antibody were from R&D System (Minneapolis, MN). Luciferase assay kit was from Promega (Madison, WI). Metafectene transfection reagent was from Biontex Lab (GmbH, Planegg/Martinsried, Germany). SMARTpool RNA duplexes corresponding to Src, TRAF2, ERK2, p38 MAPK, JNK2, and scrambled #2 siRNA were from Dharmacon Research Inc (Lafayette, CO). Anti-phospho-IKKα/β, anti-phospho-NF-κB p65 (Ser536), anti-phospho-c-Src, anti-phospho-ERK1/2, anti-phospho-p38 MAPK, anti-phospho-JNK1/2, and anti-phospho-IκB-α antibodies were from Cell Signaling (Danver, MA). anti-NF-κB (p65), anti-lamin A, anti-TRAF2, anti-TNFR1, anti-c-Src, anti-ERK2, anti-p38, anti-JNK2, anti-IκB-α, and anti-sICAM-1 antibodies were from Santa Cruz (Santa Cruz, CA). The anti-GAPDH antibody was from Biogenesis (Boumemouth, UK). Actinomycin D (Act.D), cycloheximide (CHI), PP1, U0126, SB202190, SP600125, GM6001, MMP2/9 inhibitor, and Bay11-7082 were from Biomol (Plymouth Meeting, PA). Enzymes and other chemicals were from Sigma (St. Louis, MO).
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6

Investigating NF-κB Signaling in HepG2 and MEF Cells

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HepG2 cells or MEFs were treated with vidofludimus for 1 h before exposed to TNFα (20 ng/mL) for additional 30 min (for HepG2 cells) or 1 h (for MEFs). Lysates prepared were analyzed with anti-IκBα, anti-phospho IKKα/β (Cell Signal Technology), and anti-β-actin (Cell Signal Technology) antibodies by Western blotting. Nuclear extracts from the distal colon or treated MEFs were used for assessing p65 protein level using p65 antibody (Santa Cruz) with anti-Lamin B1 (Proteintech) as internal controls. Western blotting was performed as standard procedures.
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7

Immunoblotting for Cell Signaling Pathways

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Cultured cells were solubilized in lysis buffer containing 1% NP-40. Samples were then subjected to SDS–polyacrylamide gel electro-phoresis, followed by transfer to polyvinylidene difluoride membranes and subsequent immunoblotting assay. Quantification was performed by densitometry using ImageJ. The primary antibodies used were anti–phospho-p70S6k1 (no. 9205), anti-p70S6k1 (no. 2708), anti–phospho-4E-BP1 (no. 2855), anti–4E-BP1 (no. 9644), anti-eIF2α (no. 5324), anti–phospho-eIF2α (no. 9721), anti-NFATc1 (no. 8032), anti–phospho-Erk1/2 (no. 4370), anti-Erk1/2 (no. 4695), anti–phospho-JNK (no. 4668), anti-JNK (no. 9252), anti–phospho-p38 (no. 4511), anti-p38 (no. 8690), anti–phospho-Akt (no. 4060), anti-Akt (no. 4685), anti–phospho-GSK3β (no. 9323), anti-GSK3β (no. 9315), anti– phospho-IKKα/β (no. 2697), anti-IKKα (no. 2689), anti–phospho-IκBα (no. 2859), anti-IκBα (no. 4812), and anti-p65 (no. 8242) (Cell Signaling Technologies); anti–β-actin (no. sc-47778) (Santa Cruz Biotechnology); and anti-LaminB1 (MABS492) (EMD Millipore).
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8

Visualization of CARD11-BCL10-MALT1 Complex

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Purified primary B or T cells were adhered to poly-L-lysine coated slides and fixed for 30 min with 2% paraformaldehyde (Electron Microscopy Sciences), then permeabilized for 5 min in 0.1% Triton X-100/PBS. After blocking for 30 min in 1% FCS/PBS, cell spots were incubated overnight with the following Abs: anti-CARD11 (Abcam), anti-BCL10, anti-MALT1, anti-p65, anti-RelB (Santa Cruz Biotech), anti-phospho-IKKα/β (Cell Signaling Technology). Cell spots were washed 3x in PBS, then incubated with goat anti-rabbit or anti-mouse secondary Abs conjugated to AlexaFluor 488, 568, or 647 (Invitrogen) plus a 1:10000 dilution of Hoechst 33342 (30 min per Ab). Following 6x PBS washes, coverslips were attached using Fluoromount (Southern Biotech). Fluorescent images were acquired on a Zeiss 710 confocal laser scanning microscope using a 63x oil immersion objective, and analyzed using Zeiss ZEN software. Jurkat or BJAB cells transfected with Venus-CARD11 were prepared and analyzed in similar fashion; CARD11-FLAG was visualized after staining with an AlexaFluor 647-conjugated anti-FLAG Ab (Cell Signaling Technology).
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9

Transcription Factor Activation Assay

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Tris-base, Gly, NaCl, SDS, MTT, and BSA were purchased from Sigma-Aldrich (St. Louis, MO, USA). The LightShift® Chemiluminescent EMSA Kit was purchased from Thermo Fisher Scientific Inc. (Waltham, MA, USA). Anti-phospho-IKKα/β, anti-IKKβ, anti-IκBα anti-IKKα, anti-phospho-IκBα antibodies were purchased from Cell Signaling Technology (Beverly, MA, USA). Anti-phospho-p65, anti-p65, anti-survivin, anti-Bcl-2, anti-Bcl-xl, anti-COX-2, anti-VEGF, anti-MMP-9, anti-PARP, anti-Lamin B, and anti-β-actin antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Alexa Fluor® 594 donkey anti-rabbit IgG (H + L) antibody was obtained from Life Technologies (Grand Island, NY, USA). The FITC Annexin V Apoptosis Detection Kit I was purchased from (BD Biosciences, Becton-Dickinson, Franklin Lakes, NJ, USA).
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10

Lipopolysaccharide-Induced Inflammatory Signaling

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BA (purity ≥98%) was purchased from Psaitong (Beijing, China). Dimethyl sulphoxide (DMSO) and LPS were purchased from Sigma-Aldrich (St. Louis, MO). Antibodies used for western blotting were as follows: anti-iNOS/NOS Type II (#610332; BD Biosciences, San Jose, CA); anti-cyclooxygenase (COX)-2 (#160106), anti-phospho-IKKα/β (S176/180, 16A6, #2697P), anti-phospho-IκBα (Ser32, #2859), anti-IκBα (44D4, #4814), anti-phospho-ERK1/2 (Thr202/Tyr204, #9101), anti-ERK1/2 (#9102), anti-phospho-p38 MAPK (Thr180/Tyr182, #4511), anti-p38 MAPK (#9212), anti-phospho-SAPK/JNK (Thr183/Tyr185, #9251), anti-JNK2 (56G8, #9258) and anti-NF-κB p65 (D14E12, #8242) (Cell Signaling Technology, Beverly, MA); anti-IKKα (CHUK, #A2062; ABclonal Technology, Woburn, MA); anti-β-tubulin (#CW0098A) and anti-GAPDH (#CW0266A) (CWBiotech, Beijing, China); and anti-histone H2B (Santa Cruz Biotechnology, Inc., Dallas, TX).
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