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24 protocols using caspase 3

1

Cytoplasmic and Nuclear Protein Isolation

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The cytoplasm and nuclei in LV tissue and RAW264.7 macrophages were isolated using a nuclear separation kit (Njjcbio) according to a previously described protocol [19 (link)]. Briefly, homogenate was collected from LV tissue and cells that were lysed in lysis buffer and further centrifuged at 1000 × g for 10 minutes. The pellets in the bottoms of the tubes contained the nuclei, and the supernatant contained the cytoplasm.
After the cytoplasm, nuclei, LV tissue, and HL-1 cardiomyocytes were, respectively, lysed in RIPA lysis buffer containing 10% protease inhibitors and 10% phosphatase inhibitors, the total protein was obtained and quantitated using a BCA Protein Assay Kit. After separation by electrophoresis on 10% SDS polyacrylamide gels, the proteins were transferred to PVDF membranes. Then, the protein expression of IL-16 (Abcam), Bax, Bcl-2, cleaved caspase-3, caspase-3, and GAPDH (all three from GeneTex) in total LV tissue, the protein expression of p-p65 and GAPDH (both from Abcam) in the cytoplasm, the protein expression of p-p65 and PCNA (GeneTex) in the nuclei, and the protein expression of Bax, Bcl-2, cleaved caspase-3, caspase-3, and GAPDH in HL-1 cardiomyocytes were measured using primary antibodies as indicated in parentheses. After further incubation with the secondary antibodies, the target proteins were detected and analyzed.
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2

Western Blot Analysis of Apoptosis Regulators

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Monoclonal antibodies against Bcl-2 and Bax were purchased from Santa Cruz Biotechnology (USA). The polyclonal antibodies used were against CDK4 (Santa Cruz Biotechnology), cyclin D1 (Santa Cruz Biotechnology), CDK2 (Santa Cruz Biotechnology), cyclin E (Santa Cruz Biotechnology) caspase-3 (GeneTex, USA), poly ADP-ribose polymerase (PARP, GeneTex), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, Bioworld Technology, USA).
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3

Western Blot Analysis of Protein Expression

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Protein samples were separated by 8%, 10%, or 12% sodium dodecyl sulfate-polyacrylamide gels (SDS-PAGE) and then transferred onto PVDF membranes (EMD Millipore, Burlington, MA, USA). After being blocked with 5% non-fat milk, the membranes were incubated with the following primary antibodies at 4°C overnight: α-tubulin (GeneTex, Irvine, CA, USA), collagen I (GeneTex), α-SMA (Proteintech, Chicago, IL, USA), TGF-β (Cell signaling technology, Danvers, MA, USA), TNF-α (GeneTex), NLRP3 (Proteintech), caspase-1 (Proteintech), IL-18 (Proteintech), IL-1β (Proteintech), caspase-3 (GeneTex), caspase-8 (GeneTex), caspase-9 (GeneTex), and BCL-2 (GeneTex). Membranes were then incubated with HRP-conjugated mouse anti-IgG (EMD Millipore) or HRP-conjugated rabbit anti-IgG (EMD Millipore) secondary antibodies for 1 h. Membranes were developed using ECL detection reagent (EMD Millipore). Relative protein levels were quantified using Image J (Version 1.46, National Institute of Health, Bethesda, MD, USA), and protein densitometry were expressed relative to that of α-tubulin.
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4

Apoptosis Pathway Protein Detection

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The following antibodies were used for western immunoblotting: Actin (1:5000, Millipore, Billerica, MA, USA), Bip (1:1000, BD Biosciences, San Jose, CA, USA), Caspase-3 (1:250, Gene Tex, Irvine, CA, USA), Caspase-8 (1:250, BD Biosciences, San Jose, CA, USA), Caspase-9 (1:1000, BD Biosciences, San Jose, CA, USA), Caspase-12 (1:1000, Gene Tex, Irvine, CA, USA), DR4 (1:1000, Gene Tex, Irvine, CA, USA), DR5 (1:2000, Gene Tex, Irvine, CA, USA), VCP (1:1000, Abnova, Taipei, Taiwan, ROC), Anti-rabbit IgG (1:10,000, GE Healthcare, Mickleton, NJ, USA), and Anti-mouse IgG (1:10,000, GE Healthcare, Mickleton, NJ, USA). Annexin V conjugated with FITC was bought from the Strong Biotech Corporation in Tainan, Taiwan. Chemiluminescence ECL detection system was purchased from GE Healthcare Bio-Sciences AB in Uppsala, Sweden. Dulbecco’s Modified Eagle Medium, McCoy’s5A, and fetal bovine serum were purchased from GIBCO, Grand Island in NY, USA. MTT was bought from Merck in Darmstadt, Germany. Propidium iodide was purchased from Sigma, Saint Louis in MO, USA. PVDF membrane was bought from Stratagene, La Jolla in CA, USA. TUNEL reaction mixture was purchased from Rochel in Mannheim, Germany.
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5

Western Blot Analysis of Apoptosis Markers

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The cell lysates treated with X.E.E. or X.H.E. at the indicated concentrations for various periods of time were prepared for immunoblotting of LC3, p53, Caspase 3, Bcl2, Bcl2-associated X protein (Genetex, USA). Western blot analysis was performed as previously reported [29 (link)]. The original blots can be referred in the additional file 1.
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6

Protein Expression Analysis of ZNC97018978

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Total proteins were extracted from cells treated with ZNC97018978 using RIPA lysis buffer (Solarbio, R0010), and the supernatant collected from centrifugation (13,000 rpm, 10 min) was analyzed by BCA assay kit to examine protein concentration. Electrophoresis (10% separation gel and 5% spacer gel) was performed to separate proteins, which were then transferred to a biofilm. Antigenantibody reactions were achieved by addition of primary antibodies overnight at 4 ℃. Hybridization was obtained with secondary antibodies for 1.5 h at 37 ℃. ECL method was used to visualize the protein bands. Image J was applied to perform quantitative analysis. Primary antibodies included AURKA (GeneTex, GTX13824), Caspase-3 (GeneTex, GTX110543), Bax (Abcam, ab32503), Bcl-2 (Abcam, ab196495), CDK1 (Abcam, ab18) and β-actin (Immunoway, YM3028).
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7

Evaluating MM Cell Apoptosis

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MM cells were treated with either emodin (30 μM), carfilzomib (5 nM), or a combination of both for 24 h, then washed twice with ice-cold PBS. Proteins were isolated from cell lysates using RIPA lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) containing 50 mM Tris–HCl, pH 7.5, 150 mM NaCl, 0.5% sodium deoxycholate, 1% NP-40, 0.1% SDS, and a protease inhibitor cocktail (Cyrusbio, New Taipei, Taiwan) and the protein concentration was determined by the Bradford assay (Bio-Rad, Contra Costa County, CA, USA). Thirty μg protein was separated by 10% SDS–PAGE, then immunoblotted using the following antibodies: PARP (GeneTex, Hsinchu, Taiwan), Caspase-3 (GeneTex, Hsinchu, Taiwan), LC3B (Cell Signaling Technology, Topsfield, MA, USA), and p62 (Cell Signaling Technology, Topsfield, MA, USA). GAPDH (Cell Signaling Technology, Topsfield, MA, USA) and β-actin (Cell Signaling Technology, Topsfield, MA, USA) were used as controls.
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8

Protein and Tumor Immunoblotting Analysis

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Protein or tumor extracts (20 μg) were subjected to SDS-PAGE and probed with the following antibodies: C/EBP-β (directed against the common C-terminus of LIP and LAP, Santa Cruz Biotechnology Inc., Santa Cruz, CA), CHOP/GADD153 (Abcam, Cambridge, UK), TRB3 (Proteintech, Chicago, IL), caspase-3 (GeneTex, Hsinhu City, Taiwan), β-tubulin (Santa Cruz Biotechnology Inc.). To detect ubiquitinated C/EBP-β, 100 μg protein extracts were immunoprecipitated overnight with the anti-C/EBP-β antibody, using 25 μl of PureProteome Magnetic Beads (Millipore). Immunoprecipitated samples were then probed with an anti-mono/polyubiquitin antibody (Axxora). Blotting was followed by the peroxidase-conjugated secondary antibody. The membranes were washed with Tris-buffered saline/Tween 0.01% v/v and proteins were detected by enhanced chemiluminescence. Band density was calculated using ImageJ software (http://www.rsb.info.nih.gov/ij/).
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9

Western Blot Analysis of Apoptotic Proteins

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The cells were collected by a mixture of RIPA buffer and protease inhibitor (100:1). To get total protein, cells were broken up by Selecta Sonopuls and centrifuged after ultrasonication. Protein concentration was determined by BCA method. Protein samples were separated by polyacrylamide gel and then transferred onto NC membrane (Millipore). The membrane was blocked in 5% nonfat milk at RT for 1 h, and then probed with primary antibodies. Primary antibodies against bax (1: 1000, GeneTex), bcl2 (1: 1000, GeneTex), caspase-3 (1: 1000, GeneTex), and casapase (1: 1000, GeneTex) were incubated overnight at 4 °C. Secondary antibodies (1: 10,000, abcam) was incubated for 50 min. Bands were visualized using Western Bright ECL (Advansta) and captured with ImageQuant Chemiluminescent Imaging System, LAS 500 (GE Healthcare Bio-sciences AB). The relative band intensity was quantified with imageJ2 software and normalized to β-actin.
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10

Western Blot Protein Analysis

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Antibodies against iNOS (Novus Biologicals, Littleton, CO, USA), p-p44/42 mitogen-activated protein kinase (Cell Signaling Technology, Inc., Danvers, MA, USA), caspase-3 (GeneTex Inc., Irvine, CA, USA), B-cell lymphoma 2 (Bcl2) (GeneTex), p-AKT (Santa Cruz, Dallas, TX, USA), AKT (Santa Cruz), Bcl-xL (Santa Cruz), and β-actin (Santa Cruz) were used for the western blot analysis. Proteins were quantified using the Bradford method and electrophoresed on a 12.5% (w/v) sodium dodecyl sulfate–polyacrylamide gel before being transferred to a polyvinylidene difluoride membrane (Millipore, Billerica, MA, USA). The membrane was then incubated overnight with the desired primary antibody at 4°C. The following day, after three washes with Tris-buffered saline containing 0.5% Tween 20, the Horseradish Peroxidase (HRP)-conjugated anti-IgG secondary antibody (Bio-Rad Laboratories Inc., Hercules, CA, USA) was added at the appropriate dilution. Expression of each protein was detected by exposing the membrane to Enhanced chemiluminescence (ECL) solution (GenDEPOT, Katy, TX, USA). ImageJ 2.1.4.6 (https://imagej.net/Citing) was used to determine band densities.
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