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25 protocols using anti cleaved caspase 9

1

Apoptosis Protein Expression Analysis

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The proteins were extracted from the cells using RIPA lysis buffer (Thermo Fisher Scientific, Inc.) and their concentration levels were quantified using a bicinchoninic acid protein assay kit (Beyotime Institute of Biotechnology). The proteins (40 µg per lane) were separated by SDS-PAGE on 10% gels, and were transferred onto 0.45 µm PVDF membranes (Thermo Fisher Scientific, Inc.). Following blocking with 5% non-fat milk at room temperature for 1 h, the membranes were incubated with primary antibodies overnight at 4°C. The following primary antibodies were used: Anti-Bax (Abcam; cat. no. ab32503; 1:1,000), anti-Bcl-2 (Abcam; cat. no. ab32124; 1:1,000), anti-cleaved caspase 3 (Abcam; cat. no. ab2302; 1:1,000), anti-cytochrome c (Cyto C; Abcam; cat. no. ab13575; 1:1,000), anti-apoptotic protease activating factor-1 (Apaf 1; Abcam; cat. no. ab2001; 1:1,000), anti-cleaved caspase 9 (Abcam; cat. no. ab2324; 1:1,000) and anti-β-actin (Abcam; cat. no. ab8227; 1:1,000). Subsequently, the membranes were incubated with horseradish peroxidase-conjugated secondary antibody (Abcam; cat. no. ab150077; 1:200) for 1 h at room temperature. Finally, an image of the protein band was detected using ECL reagent (Santa Cruz Biotechnology, Inc.). Image-Pro Plus software (version 7, Media Cybernetics, Inc.) was used for the targets that were normalized to β-actin.
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2

Comprehensive Lung Protein Analysis

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The total protein of lung tissues and cells was collected with RIPA buffer (Servicebio, Wuhan, China) with cocktail and phosphatase inhibitors (Thermo Fisher Scientific, Wuhan, China), followed by electrophoresed through 8–12% sodium dodecyl sulfate–polyacrylamide gel and then transferred to 0.45 μm PVDF membrane (Merck Millipore, USA). A total of 30 ug of protein was used for western blot experiments. After blocked with 5% milk, the membrane was immunoblotted with following primary antibodies(Except for labeled, all from Cell Signaling Technology, MA, USA) at 4 °C overnight: anti-ERRα (1:1000), anti-ZO-1 (1:1000; Abcam), anti-VE-cadherin (1:1000), anti-Occludin(1:1000), anti-JAM-A(1:1000; Abcam), anti-Sirt3 (1:1000), anti-Bcl-2 (1:1000), anti-Bax (1:1000), anti-Smac (1:1000), anti-Cytochrome c (1:1000), anti-caspase 3 (1:1000), anti-cleaved caspase 3 (1:500), anti-caspase 9 (1:1000), anti-cleaved caspase 9 (1:500), anti-LC3A/B(1:1000), anti-Beclin1 (1:1000), anti-p62 (1:1000), or anti-GAPDH (1:10000, Abcam, internal control). After incubated with the HRP-conjugated secondary antibodies at 25℃ for 1 h, the immunoblots were visualized using the ECL system. The gray value was analyzed using the Image J and calculate the relative protein level based on the density ratio of the target protein to GAPDH (internal control).
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3

Western Blot Analysis of Apoptosis Markers

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Proteins were extracted from cell lysates using RIPA lysis Buffer and the protein concentration was measured using the Enhanced BCA Protein Assay Kit (Beyotime) following to the manufacturer’s recommendations. Proteins were denatured by heat, and then separated by SDS-PAGE electrophoresis, finally transferred to PVDF membranes. The membranes were blocked using 1% bovine serum albumin solution for 1 h at room temperature, and then incubated with primary antibodies, including anti-cytochrome c (1:1000; Abcam), anti-cleaved caspase-9 (1:1000; Abcam), anti-cleaved caspase-3 (1:1000; Abcam), anti-phospho-Akt (1:1000; Abcam), anti-Akt (1:1000; Abcam), anti-phospho-Gsk-3β (1:1000; Abcam), anti-Gsk-3β (1:1000; Abcam), anti-phospho-Stat-3 (1:1000; Abcam), anti-Stat-3 (1:1000; Abcam) anti-COXIV (1:1000; Abcam) and anti-β-actin (1:1000; Zhongshan Jinqiao Biotechnology, Beijing, China) at 4°C overnight, followed by incubation with HRP-conjugated secondary antibody (1:5000; Zhongshan Jinqiao Biotechnology, Beijing, China) at room temperature for 30 min. Protein bands were detected using a BeyoECL Plus Kit (Beyotime) following to the manufacturer’s protocols. Relative densitometry was analyzed using Image J2x analysis software (NIH, U.S.A.).
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4

Western Blot Analysis of Apoptosis Markers

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The tissues and cells were smashed and homogenized with RIPA (Beyotime). After centrifugation, the supernatant containing protein was collected. Protein concentrations were measured by using the BCA protein concentration Kit (Beyotime). After 50 μg protein was denatured at 100˚C for 10 minutes, SDS‐PAGE electrophoresis was performed for protein separation, and then, the protein was transferred to PVDF membrane. The PVDF membrane was blocked by 5% skim milk for 1 hour and then incubated with specific primary antibodies, including anti‐APAF‐1 (1:1000; Abcam), anti‐cleaved caspase‐9 (1:1000; Abcam), anti‐cleaved caspase‐3 (1:1000; Abcam) and anti‐GAPDH (1:1000; Zhongshan Jinqiao Biotechnology), at 4°C overnight. The PVDF membrane was incubated with horseradish peroxidase labelled as goat anti‐rabbit or goat anti‐mouse immunoglobulin G (1:4000; EarthOx) at room temperature for 30 minutes. Detection of protein band was performed by using an enhanced chemiluminescence (ECL) for Western blotting kit (Beyotime) according to the manufacturer's instructions. Relative densitometry was calculated by using Image J2x analysis software.
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5

Protein Expression Analysis in Keloid Tissue

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Proteins were extracted with Radio Immunoprecipitation Assay lysis buffer containing 1 mM phenylmethylsulfonyl fluoride (Beyotime, China). Protein samples were separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and subjected to western blot analysis using the following primary antibodies: anti‐PLK4 (1:500; Abcam), anti‐p53 (1:1000), anti‐phospho‐p53Ser15 (1:1000), anti‐Cyclin B1 (1:1000), anti‐Cyclin D1 (1:1000), anti‐caspase‐3 (1:1000), anti‐cleaved caspase‐3 (1:1000), anti‐caspase‐9 (1:1000), anti‐cleaved caspase‐9 (1:1000), and anti‐β‐tubulin (1:1000). Then, the membranes were incubated with secondary antibodies (1:1000; all from Cell Signaling Technology). The protein bands were eventually visualized using an enhanced chemiluminescence detection kit (Millipore). The comparison of PLK4 expression between keloid dermis and adjacent normal skin dermis was made based on 21 biological replicates, while other western blot assays were conducted on at least three biological replicates.
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6

Fluorescence Probes and Antibodies for Cell Analysis

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Fluorescence probes, including TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling), tetraethylbenzimidazolylcarbocyanine iodide (JC-1), DAPI (4’,6-diamidino-2-phenylindole), LY294002, EdU (5-ethynyl-20-deoxyuridine), were provided by Thermo-Fisher Invitrogen (Shanghai, China). Polybrene, antibiotics, puromycin and medium were purchased from Sigma-Aldrich (St. Louis, MO). PF-562271 was provided by MCE China (Shanghai, China). The primary antibodies used were following: anti-MXRA5 (1:1000; LS‑C373823, LSBio, Shanghai, China), anti-MXRA7 (1:1000; TA336144, OriGene, Beijing, China), anti-β-actin (1:2000; Abcam), anti-GAPDH (1:2000; Cell Signaling Technology), anti-cleaved-poly (ADP-ribose) polymerase (PARP) E51 (1:1000; #32064; Abcam), anti-cleaved-Caspase 9 (1:1000; #2324; Abcam), anti-E-Cadherin (1:1000,#3195; Cell Signaling Technology), anti-N-Cadherin (1:1000; #245117;Abcam), anti-Vimentin (1:1000; #92547; Abcam), anti-p-Akt Ser-473 (1:1000; #4060; Cell Signaling Technology), anti-S6 (1:1000; #2217, Cell Signaling Technology), anti-phospho-S6 (1:1000; #4858, Cell Signaling Technology). Other antibodies were described previously [33 (link)–35 (link)].
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7

Immunoblot Analysis of Apoptotic Markers

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Myocardial tissue and AC16 cells were homogenized in an ice-cold lysis buffer. After homogenization, the lysates were centrifuged. The supernatant was saved and separated by electrophoresis on SDS-PAGE and transferred onto polyvinylidene difluoride-plus membranes. After blocking buffer, the immunoblots were probed with anti-T50 phosphorylation of Cytc(CL090701, PTM Bio), anti-Cytc(#ab13575, Abcam), anti-Cleaved Caspase-3(#ab184787, Abcam), anti-Caspase-3(sc-7272, Santa Cruz Biotechnology), anti-Cleaved Caspase-9(#ab2324, Abcam), anti-Caspase-9(sc-56076, Santa Cruz Biotechnology), anti-BCL-2(sc-7382, Santa Cruz Biotechnology), anti-BCL-XL(sc-8392, Santa Cruz Biotechnology), anti-Bax(sc-7480, Santa Cruz Biotechnology), and anti-GAPDH(60004-1-lg, Proteintech) antibodies overnight at 4° C, followed by incubation with fluorescent-conjugated secondary antibodies(A0208, Beyotime) at room temperature for 1 hour.
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8

Protein Expression Analysis by Western Blot

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Cells were digested with pre-cooled RIPA lysate and protease inhibitors (Roche, Mannheim, BW, Germany) to extract total proteins and measure concentrations using the BCA method. SDS-PAGE was used to separate lanes containing 20 μg of proteins. Proteins were transferred to polyvinyl fluoride membranes (Millipore, Billerica, MA, USA) and then incubated in blocking buffer (5% skimmed milk) for 1 h. Membranes were then probed with anti-Bcl-2 (ProteinTech, 1:500), anti-Bax (ProteinTech, 1:500), anti-Cytc (Abcam, 1:500), anti-cleaved-caspase 9 (Abcam, 1:500) and anti-cleaved-caspase 3 at 4 °C overnight. The membranes were washed three times, each time for 10 minutes and then they were incubated in anti-rabbit IgG (Abcam, 1:5000) at room temperature for 45 minutes. The specific bands were revealed using the EC3 Imaging System (Analytik Jena US LLC, USA). Gel-Pro-Analyzer software was used to measure each band’s optical density.
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9

Western Blot Analysis of Cell Signaling

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Total protein was isolated from cell lysates by using RIPA buffer, and quantified by BCA protein assay kit (Beyotime, Shanghai, China). Proteins were resolved on 10% SDS-PAGE and then transferred onto PVDF (Bio-Rad) membranes. After blocking with 5% skim milk in TBST for 1 h, the membranes were incubated with primary antibodies at 4°C overnight. Then, the membranes were incubated with secondary anti-rabbit antibody (Abcam; 1:5000) at room temperature for 1 h. Membranes were scanned by using an Odyssey Imaging System and analyzed with Odyssey v2.0 software (LICOR Biosciences, Lincoln, NE, USA). The primary antibodies used in this study were as follows: anti-p27 Kip1 (Abcam, Cambridge, MA, USA; 1:1000), anti-Bax (Abcam; 1:1000), anti-cleaved caspase 3 (Abcam; 1:1000), anti-Bcl-2 (Abcam; 1:1000), anti-cleaved caspase 9 (Abcam; 1:1000), anti-CDK2 (Abcam; 1:1000), anti-Cyclin E1 (Abcam; 1:1000) and anti-β-actin (Abcam; 1:1000). β-actin was used as an internal control.
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10

Apoptosis Signaling Pathway Analysis

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Following treatment, whole cell lysates were acquired using RIPA lysis buffer (Beyotime Institute of Biotechnology). Protein concentration was quantified using a bicinchoninic acid Protein Assay kit (Pierce; Thermo Fisher Scientific, Inc.) and 20 µg protein was separated via 10% SDS-PAGE. The separated proteins were subsequently transferred onto nitrocellulose membranes and blocked in 5% non-fat milk for 2 h at room temperature. The membranes were then incubated with the following primary antibodies at 4˚C overnight: Anti-Bcl-2 (cat. no. ab32124; 1:1,000; Abcam), anti-Bax (cat. no. ab32503; 1:1,000; Abcam), anti-cleaved caspase-9 (cat. no. ab2324; 1:1,000; Abcam), anti-cleaved caspase-3 (cat. no. ab32042; 1:1,000; Abcam), anti-caspase 3 (cat. no. ab13847; 1:1,000; Abcam), anti-caspase-9 (cat. no. ab32539; 1:1,000; Abcam) and anti-GAPDH (cat. no. ab8245; 1:1,000; Abcam). Following primary antibody incubation, the membranes were incubated with horseradish peroxidase-conjugated secondary antibody (cat. no. 7074; 1:1,000; Cell Signaling Technology, Inc.) at room temperature for 2 h in the dark. Protein bands were visualized using an ECL Western Blotting Detection reagent (GE Healthcare) and densitometric analysis was performed using Image J software (v.1.52; National Institutes of Health).
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