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20 protocols using anti cleaved caspase 3 antibody

1

Moxifloxacin HPLC Quantification in Tablets

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Analytical–grade methanol (MeOH), acetonitrile (ACN), isopropanol (IPA), and methyl tertiary butyl ether (MTBE) were purchased from Fisher Scientific Co., Ltd (Fair Lawn, NJ, USA). Formic acid (FA) and ammonium acetate (NH4OAc) were purchased from Merck (Darmstadt, Germany). Ultrapure water was provided by Wa–Haha Corporation (Hangzhou, China). Moxifloxacin hydrochloride tablets were produced by Bayer Pharma AG (Leverkusen, Germany). Anticleaved caspase–3 antibody was obtained from Abcam (ab2302).
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2

Western Blot Analysis of Renal Podocyte Proteins

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Renal cortex and cultured podocyte were lysed by lysis buffer on ice. Equal amounts of protein (20 μg per lane) were subjected to SDS-PAGE and then transferred to polyvinylidene difluoride membranes. The membranes were blocked by 5% nonfat dry milk in PBS + 0,05% Tween 20. After that, the membranes were incubated with primary antibodies at 4°C overnight. After washing with PBS, peroxidase secondary antibody was added and incubated for 1 h at room temperature. Antibodies are the following: anti-Nox4 antibody (Abcam, UK), anti-P38 antibody (Abcam, UK), anti-P-P38 antibody (Abcam, UK), anti-Bax antibody (Abcam, UK), anti-Bcl-2 antibody (Abcam, UK), and anti-cleaved caspase-3 antibody (Abcam, UK). The blots were visualized with LumiGLO reagent and peroxide, followed by exposure to X-ray film. Western Blot analyses were performed at least in triplicate.
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3

Assessing Apoptosis in Hydrogel Formulations

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Apoptosis levels of cells in different hydrogel formulations were assessed using chromogenic IHC for active caspase-3 (Collagen IHC paragraph) and TUNEL. For IHC, rabbit polyclonal Anti-Cleaved Caspase-3 antibody (ab49822; Abcam) was used at a dilution of 1 : 5,000. Immunostaining was validated by processing the mouse growth plate as an antigen positive/negative tissue control and a negative isotype control (Collagen IHC paragraph). For TUNEL, the Click-iT™ Plus TUNEL Assay for In Situ Apoptosis Detection, Alexa Fluor™ 488 dye (Thermo Fisher Scientific) was used according to the manufacturer’s instructions. TUNEL staining was validated by processing positive controls, treated with DNAse I, Amplification Grade Kit according to Manufacturers Instructions (Fisher Scientific™) for 30 min to induce DNA breaks, and negative controls, processed without the TdT enzyme to ensure the TdT reaction would not proceed alongside experimental sections. Active caspase-3 and TUNEL positivity were quantified using 20× objective-lense-images images of three regions of interest per hydrogel. 63× objective-lense-images images were used for the figures to highlight positive and negative cells stained with active caspase-3 or nuclei co-stained with DAPI and TUNEL.
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4

Quantitative Analysis of Tumor Microenvironment

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For analyses of endothelial and perivascular cells, tumor tissues containing the total areas of CD31 (clone DIA-310, Dianova, Germany) positive endothelial cells and α-smooth muscle actin (α-SMA) (Sigma-Aldrich, Saint Louis, Missouri, USA) positive pericytes were identified by scanning tumor sections under ×10 magnification and were counted in five random fields under ×200 magnification. CD8+ lymphocytes were detected using anti-CD8b antibody (eBioscience). Five random fields were selected from the tumor center, which did not include the edge of the tumor. Hypoxia was identified and quantified using immunostaining for anticarbonic anhydrase (CA)-IX (rabbit monoclonal; dilution, 1:100, Abcam). These data were analyzed using ImageJ (US NIH) and Photoshop (Adobe Systems, San Jose, California, USA) software. Analysis was performed using a laser-scanning confocal microscope (Olympus, FV-1000). Anticleaved caspase-3 antibody (Abcam) was used to assess the cell apoptosis in the tumor tissues, and antiphospho-STAT3 antibody (Abcam) for quantitative assessment of p-STAT3. For the latter, immunostained whole slide tumor sections were scanned on a Hamamatsu NanoZoomer S360 slide scanner. For quantification purpose, whole images were analyzed for at least three representative areas of vital tumor which was defined as region-of-interest.
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5

Western Blot Analysis of Protein Expression

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At 48 h after transfection, cells were harvested and total proteins were isolated with RIPA reagents (Thermo Scientific). The protein concentration was detected using a bicinchoninic acid protein assay reagent kit (Pierce, Rockford, IL) according to the manufacturer’s instructions. Equal amount of proteins per sample were separated by SDS-polyacrylamide gel electrophoresis, and then transferred onto a polyvinylidene fluoride membrane (Millipore, Billerica, MA). The membranes were blocked with 5% nonfat dry milk powder in Tris-buffered saline containing 0.1% Tween-20 (Tris 20 mM, NaCl 150 mM, and Tween 20 0.1%, pH 7.6; TBST) for 1 h at room temperature, and then incubated with anti-MFN2 antibody (Abcam, Cambridge, MA), anti-PCNA antibody (Santa Cruz Biotechnology, Santa Cruz, CA), anti-cleaved Caspase-3 antibody (Abcam) or anti-β-actin antibody (Sigma-Aldrich, Louis, MO) overnight at 4°C. β-actin was used as an internal control. After 3 washes with TBST (10 min each), membranes were incubated with the corresponding horseradish peroxidase (HRP)-conjugated secondary antibody (Santa Cruz Biotechnology) for 1 h at room temperature. After 3 washes with TBST (15 min each), blots were visualized with an enhanced chemiluminescence kit (Pierce, Rockford, IL) and then exposed to X-ray film. Protein bands were quantified using ImageJ software (National Institutes of Health, Bethesda, MD).
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6

Investigating the Role of m6A Modification in Diabetic Nephropathy

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The following reagents were used: transfection was performed with Lipofectamine RNAiMAX Reagent (Invitrogen Life Technologies, 13, 778-030) according to the manufacturer’s protocol. The following antibodies were used: anti-β-actin antibody (Proteintech, 66009-1-Ig); anti-m6A antibody (Synaptic Systems, 202,003); anti-METTL3 antibody (Abcam, Ab195352, ZEN-BIOSCIENCE [382,974]); anti-METTL14 antibody (Cell Signaling Technology, 51, 104); anti-WTAP antibody (Proteintech, 10200-1-AP); anti-KIAA1429 antibody (SAB, 29, 774); anti-TIMP2 antibody (Abcam, ab180630); anti-NF-κB p65 antibody (Cell Signaling Technology, 8242); anti-phospho-NF-κB p65 antibody (Cell Signaling Technology, 3033); anti-cleaved caspase3 antibody (Abcam, Ab2302); anti-NOTCH3 antibody (Proteintech, 55114-1-AP); anti-NOTCH4 antibody (Affinity, DF13597); anti-WT-1 antibody (Abcam, ab267377); anti-nephrin antibody (Abcam, ab216341); anti-podocin antibody (Abcam, ab181143); anti-MMP2 antibody (Proteintech, 10373-2-AP); anti-MT1-MMP antibody (Proteintech, 14552-1-AP); anti-IGF2BP2 antibody (Proteintech, 11601-1-AP); anti-col-Ⅳ antibody (Abcam, ab6586); and anti-fibronectin antibody (Abcam, ab6586). STZ was purchased from Sigma Chemical Company (MO, USA). The PAS kits were obtained from Solarbio (Beijing, China). Mouse Albumin ELISA Kit was obtained from Abcam Biotechnology (Cambridge, UK).
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7

ER Stress Assays in Cell Culture

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Dulbecco's modified eagle medium (DMEM) was purchased from Procell Life Science & Technology Co., Ltd (Wuhan, China). Penicillin–streptomycin and fetal bovine serum (FBS) were purchased from Shanghai BasalMedia Technologies Co., Ltd (Shanghai, China). DAB Assay Kit was obtained from ZSGB-Bio Co., Ltd (Beijing, China). Hoechst 33342/PI Assay Kit was obtained from KeyGEN Biotechnology Co., Ltd (Jiangsu, China). CCK-8 Assay Kit, EDU-594 Assay Kit, JC-1 Assay Kit and BCA Protein Assay Kit and p-IRE1α rabbit pAb were purchased from Beyotime Biotechnology Co., Ltd (Shanghai China). Anti-Cleaved Caspase-3 antibody was obtained from Abcam (Cambridge, UK). DDIT3/CHOP rabbit mAb, Caspase-3 rabbit pAb, ATF6 rabbit pAb and BiP/GRP78 rabbit mAb were purchased from ABclonal Biotechnology Co., Ltd (Wuhan, China). p-PERK pAb and PERK pAb were obtained from Thermo Fisher Scientific Co., Ltd (MA, USA).
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8

Western Blot Analysis of Liver Samples

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Liver specimens or cell cultures were lysed in RIPA buffer (Thermo Fisher scientific, Waltham, MA, USA), mixed with proteases inhibitors (Roche), for 30 min at 4°C, and then, centrifuged at 13 000 rpm at 4°C for 10 min. Protein samples were separated using SDS‐PAGE and then, transferred onto PVDF membranes. After blocking, the membranes were incubated with primary antibodies (anti‐PI16 antibody, anti‐β‐actin antibody, anti‐Cleaved caspase‐3 antibody: Abcam, Cambridge, UK; anti‐PARP antibody, anti‐p38 antibody, anti‐p‐p38 antibody, anti‐AKT antibody, anti‐p‐AKT antibody: Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight. Then the membranes were washed with TBST (20 mM Tris‐HCl, 150 mM NaCl, 1% Tween‐20) and incubated with HRP‐conjugated secondary antibodies (1:5000; Abcam, Cambridge, MA, USA) for 1 hour. The protein signals were revealed using enhanced chemiluminescence (Merck Millipore, Billerica, MA, USA). All western blots were conducted at least three times, and the images are representative of consistent results.
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9

Western Blot and Immunohistochemistry for Apoptosis

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For Western blot analyses, cells were lysed in 1× LDS Sample Buffer (Invitrogen) containing a protease and phosphatase inhibitor cocktail (Thermo). Proteins were resolved by SDS-PAGE and analyzed by immunoblotting with the indicated antibodies. Proteins were visualized with horseradish peroxidase-conjugated secondary antibodies (Amersham Biosciences) and an enhanced chemiluminescent substrate kit (Thermo). For immunohistochemistry (IHC), lungs were perfused with 10% formalin overnight and then stored in 70% ethanol. Lungs were embedded in paraffin, sectioned at 5 μm, and stained for cleaved caspase-3 by the Department of Pathology in Brigham and Women's Hospital.
Anti-Chk1 antibody was obtained from Cell Signaling, anti-β-actin antibody from Sigma, and Anti-cleaved caspase-3 antibody from Abcam.
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10

Ovarian Cell Proliferation and Apoptosis

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Adult wild-type and Thy1.2-AMHTg/0 ovaries were immersion-fixed in Bouins’ fixative, paraffin-embedded and serially sectioned at 5 µm thickness. Paraffin was removed from slides with xylene followed by graded ethanol solutions. Antibodies were applied in PBS with 0.08%w/v Tween20 (Sigma-Aldrich, Cat# P1379, Kenilworth, NY, USA) and 1%w/v bovine serum albumin. Anti-cleaved caspase-3 antibody (Abcam, Cat# ab2302, Cambridge, UK) was applied at 1 µg/ml and anti-PCNA antibody (Santa Cruz, Cat# SC-56, Santa Cruz, CA, USA) was applied at 0.1 µg/ml, overnight at 4°C. Secondary antibodies (4 µg/ml biotinylated donkey anti-rabbit IgG, Abcam, Cat# ab6801 or 1:500 biotinylated donkey anti-mouse IgG, Jackson Immuno Research Lab, Cat# 715-065-151, West Grove, PA, USA) and streptavidin-biotin-HRP complex (1:200, GE Healthcare, Cat# RPN1051, Chicago, IL, USA) were each applied for 1 h at room temperature. Immunoreactivity was visualized with diaminobenzidine (DAB substrate kit, Vector Labs, Cat# SK-4100, Newark, CA, USA) and the sections were counterstained with haematoxylin.
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