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8 protocols using cytochrome c cyt c

1

Diosgenin-Induced Apoptosis Mechanisms

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Diosgenin, RIPA buffer was obtained from Sigma Aldrich (St. Louis, MO, USA). RPMI-1640, DMEM medium, fetal bovine serum (FBS), trypsin, penicillin, and streptomycin were purchased from Gibco (Rockville, MD, USA). PI (propidium iodide), Annexin V-FITC/PI apoptosis detection kit, z-VAD-fmk, MTS, Hoechst 33258, and AO/EB (acridine orange/ethidium bromide) were purchased from Abcam (Cambridge, United Kingdom). 5-Ethynyl-2-deoxyuridine (EdU) was obtained from RiboBio (Guangzhou, China). The primary antibodies against GAPDH, Bax, Bcl-2, Caspase- 3, p21, PARP-1, cytochrome c (CYT C), COX IV, β-catenin and GSK3β were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Other antibodies were from Abcam. Hematoxylin–Eosin Staining Kit was from Solarbio (Beijing, China). The EliVision kit was from Maixin Biotech (Fuzhou, China).
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2

Apoptosis and Signaling Pathway Analysis

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Fetal calf serum (FCS) and RPMI 1640 were purchased from Gibco-BRL (Invitrogen Life Technologies, Carlsbad, CA, USA). MTT, dimethyl sulfoxide (DMSO), RNase A and Annexin V/propidium iodide (PI) apoptosis kits were from Sigma (St. Louis, MO, USA). Monoclonal antibodies to B-cell lymphoma 2 (Bcl-2; mouse anti-rabbit; 1:1,000), Bcl-2-associated X protein (Bax, mouse anti-rabbit; 1:1,000) and GAPDH (rabbit anti-mouse; 1:10,000) and polyclonal antibodies to poly(ADP ribose) polymerase (PARP; sheep anti-rabbit, 1:1,000), caspase-3 (mouse anti-rabbit, 1:500), caspase-8 (sheep anti-rabbit, 1:500), caspase-9 (mouse anti-rabbit, 1:500) and cytochrome c (Cyt-c; sheep anti-rabbit, 1:1,000) were supplied by Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA). Polyclonal mouse anti-rabbit antibodies targeting phosphorylated (p)-ERK (1:1,000), p-Janus kinase (JAK; 1:1,000) and p-signal transducers and activators of transcription (STAT)3 (1:1,000) were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA).
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3

Western Blotting Analysis of Cellular Signaling

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After the indicated treatment, the cells were harvested and lysed with ice-cold lysis buffer containing protease inhibitor cocktail (Roche, Mannheim, Germany). The protein concentration of the lysates was determined by a Protein Assay Kit (Thermo, Rockford, Illinois, USA), and equal amounts of protein were separated on a 10% sodium dodecyl sulfate–polyacrylamide electrophoresis gel and transferred to a nitrocellulose membrane. Nonspecific protein binding was blocked with 5% bovine serum albumin (BSA) for 1 h at room temperature. The membranes were then incubated with specific AMPKα (1:1000), phospho-AMPKα (p-AMPK; Thr172; 1:1000), p62 (1:1000), poly (ADP-ribose) polymerase (PARP), cleaved PARP (1:1000, Cell Signaling Technology, Massachusetts, USA), LC3 (1:1000), phospho-p70 S6 kinase (Thr389; 1:500, Abcam, Massachusetts, USA), cytochrome c (Cyt-c; 1:1000), Bcl-2 (1:1000), Bax (1:1000, Santa Cruz, State of California, USA), and β-actin (1:2000; MultiSciences, Hangzhou, China) primary antibodies overnight at 4 °C. The membranes were washed the next day and incubated with secondary antibodies at room temperature for 1 h. After being washed with phosphate-buffered saline (PBS) three times, the membranes were incubated with secondary antibodies. The immunoblots were detected by the Odyssey Infrared Imaging System, and the data were quantified with ImageJ software.
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4

Apoptosis Inducers and Inhibitors Protocol

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APG-1252-M1, APG-1252 (prodrug of APG-1252-M1 for in vivo study) and APG-3526 were provided by Ascentage Pharma Group Inc. (Suzhou, China). ABT263, ABT199 and S63845 (MIK665) were purchased from MedChemExpress (Monmouth Junction). AZD5991 was purchased from Selleckchem (Houston, TX). The caspase inhibitors, CBZ-Val-Ala-Asp-fluoromethyl ketone (z-VAD-fmk) and Z-lle-Glu(Ome)-Thr-Asp(OMe)-fluoromethyl ketone (z-IETD-fmk), were purchased from Enzyme System Products (Livermore, CA). CYD-2-11 was provided by Dr. X. Deng (Emory University, GA). BMH was purchased from Thermo Scientific (Rockford, IL). Rabbit antibodies against caspase-8, caspase-3, PARP, Smac, PUMA and DR5 (D4E9) were purchased from Cell Signaling Technology (Beverly, MA). Mouse antibodies against Bcl-2, Bax (N-20), Mcl-1, cytochrome C (Cyt C) and rabbit anti-Bcl-XL antibodies were purchased from Santa Cruz Biotechnology Inc. (Dallas, Texas). Bim antibody was purchased from EMD Millipore (Burlington, MA). Mouse monoclonal DR4 antibody (B-N28) was purchased from Cell Science (Newburyport, MA). Rabbit polyclonal microtubule-associated protein light chain 3 (LC3) antibody was purchased from Novus Biologicals (Littleton, CO). GAPDH antibody was purchased from Trevigen (Gaithersburg, MD). Mouse monoclonal tubulin and actin antibodies were purchased from Sigma Chemical (St. Louis, MO).
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5

Investigating Hydrogen Sulfide Signaling

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Sodium hydrogen sulfide (NaHS), the anti-CSE antibody, PD98059 (an inhibitor of ERK), LY294002 (a PI3K inhibitor), 5-hydroxydecanoate (5-HD, a mKATP inhibitor), Chelerythrine chloride (Che, a PKC inhibitor) were purchased from Sigma Chemical Co. (St. Louis, MO, USA). The primary antibodies for anti-PKC-ε, anti-cleaved caspase-3 and -9, Bcl-2, cytochrome c (Cyt c), Na+/K+-ATPase, cyclin D1, p21Cip/WAF-1 and GAPDH were from Santa Cruz (Bergheimer, Germany). Hoechst 33342, JC-1 kit and Calcein-AM were also from Santa Cruz. The anti-ERK1/2 and PI3K-Akt-GSK-3β antibodies were obtained from Cell Signaling Technology (Danvers, USA). Senescence β-galactosidase (β-gal) staining kit was purchased from Beyotime Institute of Biotechnology (Shanghai, China). Rat advanced glycation end products (AGEs) ELISA kit was purchased from Proteintech Group (Wuhan, China). All other chemicals were from Sigma or Santa Cruz.
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6

Adipocyte Differentiation Induction

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Dexamethasone (Dex), 3‐Isobutyl‐L‐methylxanthine (IBMX), insulin, triiodothyronine (T3), Rosi, and isoproterenol (ISO) were purchased from Sigma‐Aldrich. Indo was purchased from Cayman Chemical. Dulbecco's modified eagle's medium (DMEM) and calf serum (CS) were purchased from Hyclone and fetal bovine serum (FBS) from Atlanta Biologicals. Penicillin and streptomycin (P/S) were purchased from ThermoFisher Scientific. Antibodies for UCP1 (Product # U6382), β‐AR3 (Product # SAB4500584), and β‐Actin (Product # A1978) were purchased from Sigma‐Aldrich and PGC1α antibody (Catalog # AB3242) was from Millipore Sigma. Antibodies for voltage‐dependent anion‐selective channel 1 (VDAC1) (Catalog # 98708), Cytochrome c (CYTC) (Catalog # 13156), and the manganese containing superoxide dismutase (MNSOD) (Catalog # 137254) were from Santa Cruz Biotechnology, and Antibodies for ERK1/2 (Catalog # 4695), PPARγ (Catalog # 2443), Perilipin (Catalog # 9349), and anti‐rabbit IgG horse‐radish peroxidase (HRP)‐conjugated antibody (Catalog # 7074) were from Cell Signaling Technology.
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7

Proteomic Analysis of HT29 Cells

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Total proteins were extracted from HT29 and HT29-Nrf2 cells with RIPA cell lysis buffer (Cell Signaling) on ice and quantified using Bradford standard technique. One hundred microgram of extracted proteins loaded onto 10% SDS-PAGE and transferred to PVDF membrane. Then PVDF was blocked with 5% BSA for 2 h and then incubated with primary antibodies ERK 1/2 (Santa Cruz, USA, #sc-292,838), Heme Oxygenase 1 (HO-1), (Santa Cruz, USA, #sc-136,960), Ki-67 (Santa Cruz, USA, #sc-23,900), PKLR (Santa Cruz, USA, #sc-166,228), SLC25A27 (UCP4) (Mybiosource, USA, #MBS668834), FOXO3a (Cell Signaling, USA, #2497), cytochrome c (Cyt c) (Santa Cruz, USA, #sc-13,156) and β-actin (Santa Cruz, USA, #sc-130,301) overnight at 4 °C. After several washing with TBST, the PVDF was incubated with secondary mouse IgG (Santa Cruz, USA, #516102) or mouse anti-rabbit (Santa Cruz, USA, #sc-2357) for 2 h at 37 °C. The protein bands were visualized using ECL Detection reagent (Pierce, Rockford, IL, USA). Densitometry band quantification was performed using ImageJ software.
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8

Western Blot Analysis of Apoptosis Regulators

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Cells were lysed in RIPA buffer (PBS pH 7.4, containing 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) with a protease inhibitor cocktail (Sigma-Aldrich). Forty micrograms of proteins were resolved on 4-12% NuPAGE gels run in an MES buffer system (Invitrogen, cat #NP0002) and transferred to PVDF membranes according to the manufacturer's protocol. Immunoreactive proteins were revealed by enhanced chemiluminescence with ECL Plus (Amersham, cat #RPN2133). Antibodies against BCL-2 (Cat #sc-7382), BAX (Cat #sc-7480), HIF1-α (Cat #sc-10790), BNIP3 (Cat #sc-1715), Cytochrome c (cyt c, cat #sc-13156), Lamin B (Cat #sc-374015) and SIRT1 (Cat #sc-15404) were purchased from Santa Cruz Biotechnology (Santa Cruz). The antibodies for FOXO3 (Cat #2497), phosphor-FOXO3 (Ser25) (Cat #13129) and beta-actin (Cat #4970) were obtained from Cell Signaling Technologies. The antibody to cyclophilin A (Cat #07-313) was from Upstate Biotechnology. Blots were analyzed with a LAS-3000 imaging system (Fujifilm).
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