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13 protocols using gapdh hrp

1

Immunoblotting of Innate Immune Signaling Proteins

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Primary antibodies utilized for immunoblotting were: STAT1 (clone 42H3, Cell Signaling, 1:1000), pSTAT1(Y701) (clone D4A7, Cell Signaling, 1:1000), STAT2 (clone D9J7L, Cell Signaling, 1:1000), RIG‐I (clone Alme‐1, AdipoGen, 1:1000), MAVS (Enzo Life Sciences #ALX‐210‐929‐C100, 1:500), MDA5 (clone 17, mouse monoclonal antibody raised in‐house), V5‐HRP (Invitrogen, 1:5000), beta‐actin‐HRP (clone AC‐15, Sigma Aldrich, 1:10 000), GAPDH‐HRP (Proteintech, 1:10 000) and FLAG‐HRP (clone M2, Sigma Aldrich, 1:10 000). HRP‐coupled secondary antibodies include sheep‐α‐mouse and donkey‐α‐rabbit (both GE Healthcare, 1:3000).
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2

Biochemical and Crystallographic Experiments

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Reagents for biochemical and crystallographic experiments were purchased from Fisher Scientific and Hampton Research unless otherwise indicated. Ruxolitinib (phosphate) was from LC Laboratories (R-6688, >99%), Tofacitinib (citrate) from MedChemExpress (HY-40354A, 99.1%), Baricitinib (free base) from Combi-blocks (QJ-1094, 98%), Fedratinib from MedChemExpress (HY-10409, 99.9%). The following antibodies were used for immunoblotting: His-HRP (ProteinTech, HRP-66005, 1:5,000), pJAK2 (Y1007/1008) (Cell Signaling, 3771, 1:1,000), actin (Sigma, A5441, 1:1,000), GAPDH-HRP (ProteinTech, HRP-60004, 1:10,000), anti-mouse-HRP IgG (Jackson Immuno Research, 115-035-003, 1:2,000).
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3

Western blot analysis of cellular proteins

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Whole cell lysates were prepared from floating and adherent cells using RIPA or AZ lysis buffer according to standard protocols. Total protein (30–50 μg/sample) was resolved by SDS-PAGE. Proteins were detected by a standard immunoblot protocol using the following primary antibodies: PARP, cleaved PARP, cleaved caspase 3, γH2AX, XPD, p53, HER2, pHER2 (Y11221/1222), HER3, pHER3 (Y1289), HER4, pHER4 (Y1284), EGFR, pEGFR (Y1068), Chk1, pChk1(S345), pChk2 (T68), and Chk2 (Cell Signaling Technology); pH2AX (tyrosine 142; EMD Millipore); tubulin (clone B-512; Sigma), γH2AX (Santa Cruz Biotechnology) and GAPDH-HRP (Proteintech). Each experiment was repeated with independent sample preparation a minimum of three times, and representative western blots are shown.
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4

Western blot analysis of cellular proteins

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Whole cell lysates were prepared from floating and adherent cells using RIPA or AZ lysis buffer according to standard protocols. Total protein (30–50 μg/sample) was resolved by SDS-PAGE. Proteins were detected by a standard immunoblot protocol using the following primary antibodies: PARP, cleaved PARP, cleaved caspase 3, γH2AX, XPD, p53, HER2, pHER2 (Y11221/1222), HER3, pHER3 (Y1289), HER4, pHER4 (Y1284), EGFR, pEGFR (Y1068), Chk1, pChk1(S345), pChk2 (T68), and Chk2 (Cell Signaling Technology); pH2AX (tyrosine 142; EMD Millipore); tubulin (clone B-512; Sigma), γH2AX (Santa Cruz Biotechnology) and GAPDH-HRP (Proteintech). Each experiment was repeated with independent sample preparation a minimum of three times, and representative western blots are shown.
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5

Comprehensive Immunoblotting and Immunoprecipitation Procedures

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The following primary Abs were used for immunoblotting: NLRP3 (Cell Signaling 13158, 1:1000), IL-1β (Cell Signaling 12703, 1:1000), GFP (Cell Signaling 2955, 1:1000), TFEB (Cell Signaling 4240, 1:1000), CHOP (Cell Signaling 2895, 1:1000), LC3A/B (Cell Signaling clone D3U4C, 1:1000) Histone H3 (Cell Signaling clone D1H2, 1:2000), Myc (EMD Millipore clone 9E10, 1:2000), Flag (Sigma F1804, 1:1000), ASC (Santa Cruz sc-22514, 1:1000), LAMP1 (Santa Cruz clone H3A4, 1:2000), GAPDH-HRP (ProteinTech HRP-60004, 1:5000), and actin-HRP (Sigma A3854, 1:10,000). Anti-mouse (Cell Signaling 7076) or anti-rabbit (Cell Signaling 7074) HRP-conjugated secondary antibodies were used for ECL based detection. Primary Abs for immunofluorescence were NLRP3 (Enzo AlX-804-819), ASC (Santa Cruz sc-22514), ERp72 (Cell Signaling D70D12), and TGN38 (Novus, NBP1-03495). Alexa 568 conjugated polyclonal anti-mouse (Thermo Fisher, A11004) and anti-rabbit (Thermo Fisher, A11011) were used as secondary Abs prior to fluorescent imaging. For immunoprecipitation experiments, we used GFP antibodies coupled to magnetic beads (MBL, D153-9) and Flag antibodies coupled to agarose (Sigma, A2220) to pull down tagged proteins prior to immunoblotting. Cyclosporin A (R&D Systems, 1101) and Z-VAD-FMK (Sigma, V116) were used at 10 μM overnight, and Bafilomycin A1 (Sigma, B1793) at 100 nM for 4 h.
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6

Western Blot Analysis of Tau Proteins

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Samples were transferred to fresh microcentrifuge tubes, to which appropriate volumes of 4 × NuPAGE LDS sample buffer (Thermo Fisher) containing 50 mM DTT was added and heated to 95 °C for 5 min. Samples were resolved using NuPAGE Bis–Tris Novex 4–12% gels (Life Technologies) and electroblotted to a 0.2-μm PVDF membrane using the Transblot Turbo Transfer System (Bio-Rad). Membranes were blocked with 5% milk TBS–Tween 20 before incubation with primary antibodies at 4 °C (Human tau HT7, MN1000, Thermofisher; CypB, sc-130626, Santa Cruz Biotech; Pan-tau, A0024, DAKO; AT100, MN1060, Thermofisher; GAPDH-HRP, Proteintech). Membranes were then probed with appropriate secondary antibodies conjugated with HRP for 1 h (Goat anti-mouse-HRP SA00001-1 Proteintech; Goat anti-rabbit-HRP SA00001-2 Proteintech). Membranes were washed repeatedly in TBS–0.1% Tween-20 after both primary and secondary antibody incubation. Blots were incubated with Pierce Super Signal or Millipore Immobilon enhanced chemiluminescence reagents for 5 min and visualised using a ChemiDoc system (Bio-Rad).
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7

Western Blot Analysis of Cellular Proteins

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Cells were lysed in cold RIPA buffer supplemented with 1× protease inhibitor cocktail (Roche). Lysates were kept on ice for 30 min with vortexing every 5 min and then cleared by centrifugation (25,000 × g for 20 min at 4°C). Supernatants were collected, and protein contents were quantified by a BCA protein quantification assay (Pierce). After SDS-PAGE and transfer to nitrocellulose or polyvinylidene fluoride, membranes were blocked in 5% milk in 1× PBS and 0.1% Tween-20. For anti-biotin, blocking was performed in casein. In general, primary antibodies were applied overnight at 4°C, and secondary antibodies were applied for 1 hr at room temperature. Antibodies used included CCP110 (Proteintech; 1:1,000), CEP97 (Proteintech; 1:1,000), Biotin (Biotin-HRP Cell Signaling; 1:2,000), HA (Sigma; 1:1,000), GFP (Roche; 1:1,000), tubulin-HRP (Proteintech; 1:2,000), GAPDH-HRP (Proteintech; 1:1,000), and Actin (Sigma; 1:1,000). The anti-SALL1 antibodies used detect specifically SALL1FL (R&D; aa 258–499) or the N-terminal part of SALL1.6 (link) Secondary antibodies were HRP-conjugated anti-mouse or anti-rabbit (Jackson Immunoresearch). Proteins were detected with Clarity ECL (BioRad) or Super Signal West Femto (Pierce). Quantification of bands was performed with ImageJ software and normalized against Actin or GAPDH levels. At least three independent blots were quantified per experiment.
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8

Comprehensive DNA Damage Repair Assay

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SMYD3 (12011-1-AP, Proteintech), LIG4 (A1743, Abclonal), XRCC4 (A7539, Abclonal), XLF (A4985, Abclonal), Anti-Methylated Lysine (mono and di-methyl) (ab23366, Abcam), H3 (ab1791, Abcam), γH2AX (9718 S, Cell Signaling Technology), DNA-PKcs (ab44815, Abcam), KU70 (A0883, Abclonal), KU80 (A5862, Abclonal), GFP (2956 T, Cell Signaling Technology), GFP (50430-2-AP, Proteintech), FLAG (M185-7, MBL), H3K4me2 (9725, CST), H3K4me3 (9751, CST), TUBULIN (AP0064, Bioworld), GAPDH-HRP (60004, Proteintech), Goat anti-Rabbit secondary antibody (A32733, Invitrogen).
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9

Western Blot Analysis of p38/MAPK

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Cells were washed 3 times with PBS (4°C) and lysed in RIPA buffer (ProteinSimple). Cell lysates were heated to 95°C in SDS loading buffer, and the protein concentration was determined using the RCDC protein detection assay (Bio-Rad). Proteins separated by SDS-PAGE were transferred onto polyvinylidene difluoride (PVDF) membranes (Millipore), blocked in 5% skim milk, and incubated with primary and secondary antibodies. p38/MAPK (1 : 1000, Cell Signaling Technology), p-p38/MAPK (1 : 1000, Thr180/182, Cell Signaling Technology), and GAPDH-HRP (1 : 5000, Proteintech) antibodies were used. Bands were visualized by chemiluminescence using the ChemiDocTM XRC+ Imaging System (Bio-Rad) and enhanced chemiluminescence (ECL) detection reagents (GE Healthcare).
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10

Tubulin Fractionation and Immunoblotting

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The free and polymerised tubulin fractions prepared as described in the above section were probed using mouse anti-α-tubulin (1:1000, Santa Cruz Biotechnology, USA) antibody; the GAPDH-HRP (1:5000, Proteintech, USA) in the supernatant was chosen as the internal control for the free tubulin, and the mouse anti-Porin 31HL (Ab-2) (1:2000, Calbiochem, Germany) in the Triton X-100 insoluble fraction was chosen as the control for polymerised tubulin. The tubulin fractions and whole cells were stimulated and then lysed. The protein extracts were separated using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), transferred to a polyvinylidene fluoride (PVDF) membrane, and probed with specific antibodies as follows: p38 (1:1000, Cell Signaling Technology, USA), p-P38 (1:1000, Cell Signaling Technology, USA), MAP4 (1:1000, Bethyl, USA), p-MAP4 (S768, 1:1000) (Biolegend, USA), and rabbit polyclonal antibody against p-MAP4 (S696, 1:500) or p-MAP4 (S787, 1:500). As a loading control, GAPDH was probed and visualised. The immunocomplexes were visualised and quantified using an enhanced chemiluminescence detection kit (Amersham Pharmacia, Piscataway, NJ) and horseradish peroxidase-conjugated secondary antibodies.
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