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9 protocols using z atad fmk

1

Apoptosis Induction Assay Protocols

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Tunicamycin and thapsigargin were purchased from Sigma and resuspended in DMSO. Tunicamycin was used at 0.1 µg/ml, and thapsigargin was used 0.1 µM, according to previous studies [15] (link), [37] (link). CD95 and camptothecin were purchased from BD Pharmingen and used at 5 µM per manufacturer's protocol. Caspase Inhibitor VI (Z-VAD-FMK) that inhibits all caspases was purchased from Calbiochem. Caspase-8/FLICE inhibitor (Z-IETD-FMK), Caspase-9/Mch6 inhibitor (Z-LEHD-FMK) and Caspase-12 inhibitor (Z-ATAD-FMK) were purchased from Biovision. All caspase inhibitors were dissolved in DMSO and kept at 2 mM as 1000X stock solution. For cell treatments, the aforementioned chemicals were diluted directly in corresponding media and filtered for sterile conditions.
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2

Cell Viability and Apoptosis Analysis

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The numbers of viable cells were analyzed using a Cell-Titer Blue assay (Promega, Fitchburg, WI). The caspase-12 specific inhibitor, Z-ATAD-FMK (BioVision, Milpitas, CA), was incubated prior to hydrogen peroxide (Sigma-Aldrich) stimulation. The data were expressed as a relative ratio to the control.
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3

Pharmacological Inhibition of PERK and Caspase-12 in N2a Cells

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After seeding N2a cells for 24 h, cells were pretreated with 4 µM GSK2656157 (MedChemExpress LLC, Shanghai, China) (a PERK inhibitor) and 5 µM Z-ATAD-FMK (BioVision Inc., Milpitas, CA, USA) (a caspase-12 inhibitor) for 1.5 h and 6 h, respectively. Following pretreatment with inhibitors, Lipofectamine 3000 reagent was used to transfect cells with plasmids as described previously.
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4

Nasopharyngeal Squamous Carcinoma Cell Lines

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NPC076 and NPC039 are the isolated nasopharyngeal squamous carcinoma cell lines used in this study [10 (link)]. The two cell lines were cultured in DMEM/F-12 (Invitrogen, Carlsbad, CA, USA) supplemented with 5% FBS at 37 °C under 5% CO2/95% air. The cell lines were incubated and conditioned with the following reagents for experiment control: Z-ATAD-fmk (1–3 μM, BioVision, San Francisco, CA, USA), a cell permeable caspase 12 inhibitor. BMS345541 (1–5 μM, #16667, Cayman, Ann Arbor, MI, USA), a cell permeable IKKα/β inhibitor. Multiple antibodies were purchased and applied for either immunofluorescence staining, western blotting, or coimmunoprecipitation. Antibodies for a variety of proteins are listed as follows: antibody for Casp12 (#55238-1-AP, Proteintech, Rosemont, IL, USA), IκBα, IKKα’IKKβ, p-IκBα, and p-p65 (#4812, #2682, #8943s, #9246, #3033, Cell Signaling, Danvers, MA, USA), IKKα, NEMO (#sc14A231, #sc8032, Santa Cruz, Dallas, Texas, USA), or GFP tags (#GTX628528, GeneTex, Hsinchu City, Taiwan). P-IkB Human Casp12 (hCasp12), Casp12 (GFP-tagged), is from the human Casp12 cDNA (#RG231175, OriGene, Rockville, MD, USA).
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5

Apoptosis Modulation in Aeromonas hydrophila-infected Macrophages

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The HKM were pre-treated with ER-stress alleviator (4-phenyl butyrate, 4-PBA, 10 μM), NADPH Oxidase inhibitor-apocynin (Apo, 100 μM), MPTP formation inhibitor-cyclosporin A (CsA, 5 μM, US Biological), RyR inhibitor-Dantrolene (Dant, 20 μM), iNOS-specific inhibitor (L-Nil, 50 μM, Cayman), cGMP inhibitor (LY83583, 20 μM), MUP inhibitor-Ruthenium Red (RR, 20 μM), NF-κB activation inhibitor (NF-κBi, 10 nM, Calbiochem), PKG inhibitor (KT5823, 1 μM), IP3R inhibitor-xestospongin C (Xes, 1 μM), Caspase-12 inhibitor (Z-ATAD-FMK, 10 μM, Biovision), Caspase-8 inhibitor (Z-IETD-FMK, 10 μM, Promega), Caspase-9 inhibitor (Z-LEHD-FMK, 10 μM, Calbiochem) for 1 h or flavoenzyme inhibitor-Diphenyleneiodonium (DPI, 10 μM) for 2 h prior to A. hydrophila-infection and apoptosis studied at 24 h p.i. using Hoechst 33342 (3.25 μM), AV-FITC-PI (BD-Pharmingen) and caspase-3 assay (Promega). The HKM were stained with Hoechst 33342 or AV-FITC-PI and visualized under fluorescence microscope (Nikon Eclipse 400, ×40)4 (link). The caspase-3 assay was done following manufacturer's instructions. Briefly, HKM were collected, re-suspended in lysis buffer, plated with reaction buffer and DEVD-pNA, incubated at 30°C for 5 h and absorbance read at 405 nm.
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6

Oxidative Stress and TGF-β1 in AF Cells

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AF cells were seeded into 96-well culture plates at a density of 5 × 103 cells and maintained in complete medium (DMEM/F12 with 10% fetal bovine serum; Gibco/Invitrogen, Carlsbad, CA, USA). When the AF cells reached to 90% confluence, the medium was replaced with complete medium consisting of different concentrations of H2O2 (50, 100, 200 μmol/L; 30% solution, Sangon Biotech, Shanghai, China) for various time points (0.5, 1, 2, and 4 h). Each different concentration was repeated in 5 wells. To observe the influence of TGF-β1 addition on AF cells, different concentrations of TGF-β1 (5, 10, 20 ng/mL; Peprotech, Rocky Hill, NJ, USA) were added when the above pre-designed concentrations of H2O2 were reached. The cells were pretreated by various chemical blockers, including EK1/2 inhibitor U0126 (Calbiochem, San Diego, CA, USA), p38 inhibitor SB203580 (Calbiochem, San Diego, CA, USA), JNK inhibitor SP600125 (Calbiochem, San Diego, CA, USA), autophagy inhibitor Bafilomycin A (Baf A; Biotime, Shanghai, China), apoptosis inhibitors Z-VAD-FMK (BioVision, California, USA), Z-ATAD-FMK (BioVision, California, USA), and NS3694 (Calbiochem, Billerica, MA, USA), at 2 h before the addition of H2O2 and/or TGF-β1.
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7

Saikosaponin-Induced Apoptosis Pathway

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Saikosaponin (SSa; Nacalai Tesque Inc., Kyoto, Japan) was dissolved in DMSO (Sigma Chemical Co., St. Louis, MO) to form a 10-mM stock solution and stored at –20°C until use. Propidium iodide (PI), RNase A, Hoechst 33342, cytochalasin-B, Giemsa stain, and 4’,6-diamidino-2-phenylindole (DAPI) were purchased from Sigma. Caspase colorimetric assay kits were purchased from BioVision (Palo Alto, CA). Caspase-4 inhibitors, z-LEVD-fmk and Ac-LEVD-CHO, were obtained from Enzo Life Sciences (Plymouth Meeting, PA). The caspase-12 inhibitor, z-ATAD-fmk, was obtained from BioVision. z-DEVD-fmk (caspase-3 inhibitor), z-VDVAD-fmk (caspase-2 inhibitor), and z-IETD-fmk (caspase-8 inhibitor) were obtained from Calbiochem (La Jolla, CA). The annexin V-fluorescein isothiocyanate (FITC) apoptosis detection kit was purchased from BD Biosciences (Franklin Lakes, NJ, USA).
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8

Nasopharyngeal Carcinoma Cell Lines: Isolation and Characterization

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Human nasopharyngeal carcinoma cell lines NPC076, and NPC039 are isolated from nasopharyngeal squamous cell carcinoma [35 (link)]. The cells are maintained in basal medium (DMEM/F-12 at 1:1, v/v; Invitrogen, Carlsbad, CA) supplemented with 5% fetal bovine serum in a humidified incubator at 37°C under 5% CO2/95% air. The Z-ATAD-fmk is a specific inhibitor for Casp12 purchased from BioVision or ProteinTec. The antibody for IκBα was purchased from Santa Cruz (SC-371). Other antibodies or reagents were purchased from Cell Signaling, ABcam, or Sigma Aldrich. A plasmid for cDNA-Caspase 12 (pC12) was a gift from Junying Yuan (Addgene plasmid # 35574) [11 (link)].
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9

Inhibitor Pretreatment and Plasmid Transfection

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After seeding N2a cells for 24 hr, cells were pretreated with 4 µM GSK2656157 (MedChemExpress LLC, Shanghai, China) and 5 µM Z-ATAD-FMK (BioVision Inc., Milpitas, California) for 1.5 hr and 6 hr, respectively. Following pretreatment with inhibitors, Lipofectamine 3000 reagent was used to transfect cells with plasmids as previously described.
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