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7 protocols using af 401 na

1

Western Blot Analysis of Neutrophil Proteins

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Neutrophil lysates (20–30 μg protein) were fractionated in 12% SDS–PAGE, transferred onto nitrocellulose membranes, and incubated with primary antibodies—mouse IL-1β (R&D Systems, AF-401-NA at 1:1,300), mouse Caspase-1 p10 (Santa Cruz, SC-514 at 1:200), or with antibodies targeted to the intracellular C terminus or extracellular region of P2X7R (Alomone Labs, catalog# APR 004 for the C terminal, and APR 008 for the ecto-domain, both at 1:200 dilution). These antibodies recognize mouse and human receptors. Loading controls were shown using antibodies to β actin (Sigma Aldrich A3854, 1:50 000). Reactivity was determined using HRP-conjugated secondary antibodies (Santa Cruz) and developed using Supersignal West Femto Maximum Sensitivity Substrate (Pierce). Images were cropped for presentation; full size images are presented in Supplementary Fig. 5.
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2

Immune Cell Characterization in Mouse Peritoneal Exudates

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Antibodies against NLRP3 (Adipogen, Cryo2) (Sigma, HPA012878), IL-1β (R&D systems, AF-401-NA), caspase-1 (Santa Cruz, SC-154), MAP1 (Sigma, HM-1), NEK7 (Abcam, ab133514), MAP4 (BD, 611026), α-tubulin (MBL, PM054), acetylated tubulin (Santa Cruz, SC-23950), γ-tubulin (Sigma, T5326), Tom20 (Santa Cruz, FL-145, SC-11451), ERK2 (Santa Cruz, C-14), HA tag (Santa Cruz, y-11), Flag tag (Sigma, F1804) were used for western blots. Antibodies against MARK4 (Cell Signaling, 4834) (Abcam, ab124267) (house-made by MRC-PPU, the University of Dundee, UK), NLRP3 (Sigma, HPA012878; Abcam, ab4207), ASC (Enzo, ADI-905-173) (Santa Cruz, SC-33958) were used for in situ proximity-ligation assay. Antibodies against markers CD11b (BIOLEGEND, 101217, 1 in 800 dilution), F4/80 (ebiosciences, 25-4801-82, 1 in 200 dilution), Ly6G (BD, 551461, 1 in 400 dilution), and Ly6C (AbD SeroTec, mca771a647, 1 in 400 dilution) were used for flow cytometry. See Supplementary Fig. 15d for gating strategy for peritoneal exudates.
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3

Western Blot Analysis of Cell Signaling

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Cell lysates and supernatants (reduced and denatured) were separated on 4–12% gradient gels (Invitrogen) and protein transferred nitrocellulose membrane (Amersham) for detection. Membranes were blocked with 5% skimmed milk in PBS containing 0.1% Tween 20 (PBST) for 1–2 h and were then probed overnight with primary antibodies (all diluted 1/1,000 unless noted otherwise) to mouse β-actin (Sigma; A-1978), cIAP1 (1/500 dilution, ALX-803-335;Alexis Bio-chemicals), RIPK3 (Axxora; PSC-2283-c100), RIPK1 (BD Transduction Laboratories; 610458), MLKL (in-house; 3H1), pro and mature IL-1β (R&D Systems; AF-401-NA), pro- and cleaved-caspase-1 (Santa Cruz; sc-514), Adipogen (AG-20B-0042-C100), pro-caspase-8 (in-house), cleaved caspase-8 Asp387 (9429; Cell Signaling) and Ubiquitin (3933; Cell Signaling). Relevant horseradish peroxidase-conjugated secondary antibodies were applied for 1–2 h. Membranes were washed four to six times in PBST between antibody incubations and all antibodies were diluted in PBST containing 5% skimmed milk. Membranes were developed using ECL (Millipore). For images cropped for presentation, the full-size images are presented in Supplementary Figs 9–14.
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4

Characterizing NLRP3 Inflammasome Pathway

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We purchased antibodies against NLRP3 (AdipoGen, AG-20B-0014-C100), Caspase-1 (AdipoGen, AG-20B-0042-C100), caspase-11 (Novus Biologicals, NB-120–10454), IL-1β (R&D Systems, AF-401-NA), caspase-4 (Santa Cruz Biotechnology Inc., sc-56056), caspase-5 (Santa Cruz Biotechnology Inc., sc-393346), CREB (Cell Signaling, 48H2), VE-cadherin (Santa Cruz Biotechnology, sc-6458), and β-actin (Sigma, A-5316). Polyclonal anti-SARS-CoV-2 spike glycoprotein was obtained from BEI Resources. IL-1R antagonist Anakinra (IL-1RA, #407616) was obtained from Calbiochem; Anakirna (C759H1186N208O232S10.) is a recombinant biopharmaceutical and slightly modified version of the human interleukin 1 receptor antagonist protein-IL-1RA. Albumin (catalog A7906), O-Dianisidine dyhydrochloride (catalog D3252), and protease inhibitor cocktail (catalog P8340) were from Millipore Sigma. The CytoTox 96® Non-Radioactive Cytotoxicity Assay kit (G1780) were purchased from Promega. Enhanced chemiluminescence (ECL) Western blotting Detection Reagents and nitrocellulose membranes (Hybond-ECL) were from Amersham Biosciences Corp. Lipofectamine® 3000 transfection reagents were from Invitrogen.
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5

Protein Extraction and Immunoblotting Protocol

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Cells were lysed in buffer containing 20 mM HEPES (pH 7.5), 0.5% Nonidet P-40, 50 mM KCl, 150 mM NaCl, 1.5 mM MgCl2, 1 mM EGTA and protease inhibitors. Soluble lysates were fractionated by SDS–polyacrylamide gel electrophoresis and then transferred to polyvinylidene difluoride membranes. In some experiments, cell culture supernatants were precipitated by the addition of methanol/chloroform mixture as described previously60 (link) and then immunoblotted. The following antibodies were used for detecting mouse caspase-1 (Adipogen AG-20B-0042, 1:2,000), mouse IL-1β (R&D AF-401-NA, 1:1,000), human caspase-1 (Santa Cruz SC-515, 1:500), human IL-1β (Cell Signaling 2022, 1:1,000), mouse NLRP3 (Adipogen AG-20B-0014, 1:2,000) and mouse ASC (Santa Cruz SC-22514-R, 1:500). All the blots shown are representative image of at least three independent experiments. Images have been cropped for presentation. Full size images are presented in Supplementary Fig. 20.
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6

NLRP3 and Caspase-1 Activation Assay

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We purchased antibodies against NLRP3 (AdipoGen; AG-20B-0014-C100), caspase-1 (AdipoGen; AG-20B-0042-C100), caspase-11 (Novus Biologicals; NB-120-10454), IL-1β (R&D Systems; AF-401-NA), caspase-4 (Santa Cruz Biotechnology, Inc; sc-56056), caspase-5 (Santa Cruz Biotechnology, Inc; sc-393346), CREB (Cell Signaling; 48H2), VE-cadherin (Santa Cruz Biotechnology; sc-6458), and β-actin (Sigma; A-5316). Polyclonal anti–SARS-CoV-2 spike glycoprotein was obtained from BEI Resources. IL-1R antagonist anakinra (IL-1RA, #407616) was obtained from Calbiochem; anakinra (C759H1186N208O232S10.) is a recombinant biopharmaceutical and slightly modified version of the human IL-1RA. Albumin (catalog A7906), O-dianisidine dyhydrochloride (catalog D3252), and protease inhibitor cocktail (catalog P8340) were from Millipore Sigma. The CytoTox 96 Non-Radioactive Cytotoxicity Assay kit (G1780) was purchased from Promega. Enhanced chemiluminescence Western blotting detection reagents and nitrocellulose membranes (Hybond ECL) were from Amersham Biosciences Corp. Lipofectamine 3000 transfection reagents were from Invitrogen.
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7

Western Blot Analysis of NLRP3 Inflammasome Activation

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BMDMs stimulated as per the experiment were lysed in buffer containing 20 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% NP-40 and 5 mM EDTA with fresh 1x Halt Protease inhibitor cocktail (Promega #1861279). Homogenized lysates were resolved on 14% SDS-PAGE, and transferred to 0.2 μM PVDF membrane. Membranes were blocked with 5% non-fat dry milk (w/v) and probed with antibodies diluted in 1X PBS and 0.05% Tween-20 (v/v). The antibodies used were pro-IL1β (R&D Systems, AF-401-NA), caspase-1 (Santa Cruz Biotechnology, sc-514), gasdermin D (Abcam, AB209845), β-actin (Sigma), Nlrp3 (Enzo Life Sciences, clone cryo-2), Gapdh (Sigma, G9295), Flag (Sigma, A8592), KDEL (Enzo Life Sciences 10C3), Tom20 (Abcam, AB186734), VDAC (Cell Signaling, 4866S), HSP60 (Santa Cruz, 13115). The Mm47 antibody was custom made by Thermo Fisher against the immunogenic residue 22–47 of Mm47. Membranes were probed with horseradish peroxidase-conjugated anti-mouse (Bio-Rad, 172–1011) and anti-rabbit (Bio-Rad, 170–6515) or anti-Goat (Bio-rad, 172–1034) and developed using ECL chemiluminescent substrate (Pierce).
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