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89 protocols using cytochrome c

1

Mitochondrial Protein Profiling in Cells

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Cells were lysed in RIPA lysis buffer and phenylmethanesulphonyl fluoride at 4°C for 30 min. Mitochondria were isolated using the Mitochondria Isolation Kit for Cultured Cells (Thermo Scientific, Rockford, IL, USA) and prepared for Western blot analysis. A total of 30 μg of protein was separated in a 6% to 12.5% SDS-PAGE gel, transferred to a PVDF membrane and probed with the following antibodies overnight at 4°C: caspase-9 (cat# ab202068, 1:600 dilution, Epitomics), cytochrome C (cat# ab133504, 1:400 dilution, Epitomics), caspase-12 (cat# 3282-100, 1:1000 dilution, BioVision), VDAC1 (sc-390996, 1:600 dilution, Santa Cruz), Notch1 (cat# 3282-100, 1:400 dilution, Santa Cruz), Notch2 (cat# 5732, 1:1000 dilution, Cell Signaling Technology), Hes1 (cat# ab71559, 1:400 dilution, Abcam) and Hey1 (cat# ab22614, 1:400 dilution, Abcam). After incubation with either HRP-conjugated anti-rabbit or anti-mouse antibodies, immunoreactive bands were visualized by chemiluminescence (ECL Plus; GE Health Care, Piscataway, NJ), and the membranes were exposed to light film (BioMax MR; Kodak, Rochester, NY). The β-actin antibody (1:2000 dilution; Santa Cruz) was used as a loading control.
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2

Immunoblotting of Apoptosis Regulators

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Cell lysates were extracted with cell lysis buffer (Beyotime Biotechnology, Nantong, China), and the protein concentration in the lysates was quantified using a Micro BCA Protein Assay Kit (Sangon Biotech, Shanghai, China). A total of 20–50 μg of each cell lysate sample was loaded for immunoblotting and detected by antibodies that recognize Tubulin, VDAC, AIF, SMAC/DIABLO, cytochrome c (Epitomics, Hangzhou, China), CUL1 (Santa Cruz Biotechnology, Santa Cruz, CA, USA), CDKN1B/P27, CDKN2A/P16, PARP, γH2AX, caspase3, caspase8, caspase9, BCL-2, pBCL-2 (S70), BCL-XL, MCL-1, BID, BAD, BAX, and BIM (Cell Signaling Inc., Danvers, MA, USA).
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3

Apoptosis Signaling Pathways Analysis

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MCF-7 cells were placed in a six-well culture plate at a density of 5×105 cells per well and treated with 12.5 µg/mL of each NP or with NPs plus NAC/SP600125 for 24 hours. Then, the cells were lysed using radio immunoprecipitation assay lysis buffer, and the protein concentrations of the cell lysates were measured using a bicinchoninic acid protein assay kit (Beyotime Biotechnology, Jiangsu, People’s Republic of China). Equal amounts of cell lysate protein were resolved in 12% sodium dodecyl sulfate-PAGE gels and transferred to polyvinylidene difluoride membranes (EMD Millipore, Billerica, MA, USA). Primary antibodies against the following proteins were used: JNK (Cell Signaling Technology, Danvers, MA, USA), p-JNK (Cell Signaling Technology), ERK (Cell Signaling Technology), p-ERK (Cell Signaling Technology), p38 (Cell Signaling Technology), p-p38 (Cell Signaling Technology), Bax (Proteintech, Chicago, IL, USA), Bcl-2 (Epitomics, Burlingame, CA, USA), cytochrome-c (Epitomics), caspase-3 (Epitomics), caspase-9 (Epitomics), PARP (Epitomics) and GAPDH (Proteintech).
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4

Apoptosis Signaling Pathway Characterization

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Sources of various chemicals and reagents used in these studies are as follows: BAPTA (Calbiochem); BSA (Thermo Fisher); Dulbecco’s PBS (Gibco Life Technologies); bovine liver catalase (Sigma Aldrich); CCCP (Calbiochem); CellTiter 96® Aqueous One solution (Promega); FBS (Atlanta Biologicals); oligomycin (Sigma Aldrich); Matrigel® (BD Biosciences); TBB, TBCA and thapsigargin (EMD Millipore); trypsin + EDTA (Gibco Invitrogen); and JC-1 (Life Technologies). The following antibodies were used for western blot analysis: AKT-1 phospho-Ser129 (1:1000, Epitomics 5508-1); AKT-1 (1:1000, Cell Signaling 9272); actin (1:1000, Santa Cruz sc-1616); cleaved caspase-3 (1:1000, Cell Signaling 9661); caspase-9 (1:1000, Cell Signaling 9508); lamin A/C (1:1000, Cell Signaling 2032); CKII α (1:3000, Bethyl Laboratories A300-197); CKII α′ (1:3000, Bethyl Laboratories A300-199); cytochrome c (1:10,000, Epitomics 2119-1); Bax (1:1000, Cell Signaling 2772); Bid (1:1000, Cell Signaling 2002); and Cox IV (1:1000, Cell Signaling 4850).
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5

Antibody selection for Western blot, IF, and FC

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The following rabbit anti-mouse antibodies purchased from Abcam were used for Western blotting: Nucleolin (ab22758), EGFR (ab52894), CD36 (ab133625), IFNγ (ab133566), TLR3 (ab62566), Fibrillarin (ab5821), Cytochrome C (ab133504), F4/80 (ab100790), β-actin (ab8227), and GAPDH (ab181602). The goat anti-rabbit lgG-Alexa Fluor 488 (Cat. # A27034) was purchased from Thermo Fisher for immunofluorescence. The FITC-F4/80 (Cat# 123108) antibodies purchased from Biolegend were used for flow cytometry.
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6

Mitochondrial Protein Expression Analysis

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15 μg of Mitochondrial lysates and supernatant fraction (cytosolic) were resolved by 7% SDS-PAGE for higher molecular proteins and 12% SDS-PAGE for small molecular proteins, then transferred to polyvinylidene difluoride membrane (PVDF). Membranes were blocked with 5% nonfat dried milk in TBST, incubated overnight at 4 °C with the indicated primary antibodies (HA epitope, BioLegend, 1:1000 dilution), SLC4A11 [37 (link)] (Custom, 1:500), TOM20 (SCBT, 1:1000), TIM23 (BD, 1:1000), VDAC (CST, 1:1000), UCP2 (CST, 1:1000), GLS1 (CST, 1:1000), Cytochrome c (Abcam, 1:1000), and α-tubulin (SCBT, 1:1500), washed three times in TBST (138 mM NaCl, 20 mM Tris, and 0.5% Tween 20, pH 7.6) for 10 min each, and incubated with secondary antibodies for 1 h at room temperature. After washing the membrane with TBST three times for 10 min each, the immunoreactive bands were visualized by enhanced chemiluminescence, ECL buffer (#34578, Thermo Fisher Scientific) using Gel Doc XR + system (Bio-Rad, Hercules, CA).
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7

Chaetocin Induces Melanoma Cell Apoptosis

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Human melanoma cell lines, Sk-Mel-28, A375, IGR37, LU-1205 and MV3 were purchased from Shanghai Cell Bank of Chinese Academy of Sciences, and they were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Gibco, USA), penicillin (100 IU/ml), and streptomycin (100 μg/ml) in a humidified incubator with 5% CO2 at 37°C. Human primary melanocytes were obtained Kanglang Company (Shanghai, China) and cultivated in melanocytes growth with 10% FBS. 3-[4, 5-dimethylthiazol-2-yl]-2, 5-diphenyltetrazolium bromide (MTT) and chaetocin were purchased from Sigma-Aldrich Corp. (St. Louis, MO). chaetocin was dissolved in dimethyl sulfoxide (DMSO) to prepare a 50 mM stock solution which was diluted to the final concentration with culture medium. The final concentration of DMSO was kept under 0.1% throughout the following studies, and showed no effect on cell morphology and proliferation in this study. The primary antibodies recognizing Bax, Bcl-2, procaspase-9/-3, cleaved caspase-9/-3, cytochrome c, PCNA, Nrf2, SOD2, catalase, and β-actin were purchased from Abcam Company (Cambridge, UK).
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8

Protein Extraction and Western Blot Analysis

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The extraction of cell cytoplasmic and mitochondrial fractions were performed using the Mitochondria/Cytosol Fractionation Kit (BioVision, CA, USA) according to the manufacturer’s protocol. Total cell proteins were extracted by RIPA lysing buffer (Beyotime Institute of Biotechnology, China) and protein concentration was determined by the BCA Bradford protein assay kit (Beyotime Institute of Biotechnology, China). The extracted proteins were then mixed with loading buffer and boiled for 10 min. Equal amounts of proteins (40 μg) were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene difluoride (PVDF) membranes (Millipore, Germany). After being blocked with 5% non-fat dry milk for 2 h, membranes were incubated overnight at 4 °C with primary antibodies against GAPDH (1:1000, Abcam, USA), VDAC (1:2000, abcam, USA), cytochrome C (1:500, Abcam, USA), Bcl-2 (1:500, Abcam, USA), Bax (1:800, Abcam, USA), cleaved caspase 3 (1:500, Abcam, USA), caspase 8 (1:500, Abcam, USA), cleaved caspase 9 (1:500, Abcam, USA), and then incubated with horseradish peroxidase-conjugated secondary antibody (ZSGB-BIO, China) for 2 h at room temperature. Membranes were visualized by an enhanced chemiluminescence (ECL) kit (Thermo, USA) and quantified by densitometry using an image analyzer (BandScan, USA).
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9

Mitochondrial Dynamics in Cardiomyocytes

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Mouse heart tissue and primary cardiomyocytes were analyzed by western blotting as previously described 27 (link). For mitochondrial protein isolation, mitochondria were isolated from primary cardiomyocytes with Cell Mitochondria Isolation Kits (C3601, Beyotime Biotechnology, Jiangsu, China) in strict accordance with the manufacturer's instructions. Primary antibodies against the following proteins were used: β-actin (Proteintech, China, #20536-1-AP), Mfn1 (Abcam, #ab57602), Mfn2 (Abcam, #ab56889), Opa1 (Abcam, #ab42364), Fis1 (Genetex, USA, #GTX111010), Drp1 (Cell signaling, USA, #8570), PPARα (Novus, #NBP1-04676), cytochrome C (Abcam, #ab133504), caspase-3 (Cell signaling technology, #9662), cleaved caspase-3 (Cell signaling technology, #9664) and Nox4 (Abcam, #ab133303).
RNA was extracted with RNAisoPlus (#9189Q, Takara, Japan), cDNA was synthesized with aPrimeScript™ RT Reagent Kit with gDNA Eraser (#RR047Q, Takara), and quantitative RT-PCR was performed with SYBR® Premix Ex Taq™ II (#RR820L, Takara). All procedures were performed strictly following the manufacturers' protocols. The primer sequences are as follows: Mfn2 forward CTTGAAGACACCCACAGGAACA, Mfn2 reverse GGCCAGCACTTCGCTGATAC; Actin forward GTCCCTCACCCTCCCAAAAG, and actin reverse GCTGCCTCAACACCTCAACCC.
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10

Protein Quantification and Western Blot Analysis

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Cells were lysed in a cell lysis buffer to obtain the total cellular extracts. The Pierce bicinchoninic acid (BCA) Protein Assay Kit was employed to determine the content of total protein in lysis cellular extracts (14 (link)). The sample protein was separated using 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and BCA quantified the protein sample concentration. Finally, the amount used in 10% SDS-PAGE was 20 μg. A nitrocellulose membrane (Mini-PROTEAN Tetra Cell, Bio Rad, Hercules, CA) was used to blot the SDS-PAGE. The HRP-conjugated secondary Ab or FLA9000 (Fuji Film, Minato, Japan) protein was visualized by electrochemiluminescence (ECL) using ChemiDoc-It (UVP, Upland, CA). The strip densitometry was performed using ImageJ Freeware (http://rsbweb.nih.gov/ij/). Antibodies used for blotting were Bcl-xl, 1:1,000; Bcl-2, 1:500; caspase3, 1:1,000; caspase9, 1:500 (Proteintech Group, USA); cytochrome C, 1:1,000 (Abcam, UK); and PARP-1, 1:500 (Cell Signal, USA).
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