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16 protocols using casp3

1

Apoptosis and Epigenetic Factors Analysis

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All tissue specimens were examined for pro-apoptotic factors (CASP3, TRTAIL-R1, IGFBP, BAX, and XAF1), anti-apoptotic factors (survivin, ERK, RAF1, BCL2, and MDM2), histone methyltransferase (MLL2, RIZ, EZH1, and NSD2), and histone demethylase (KDM5c, JMJD2a, UTX, and JMJD5). For this analysis, the labeled streptavidin-biotin method was performed on sections from paraffin-embedded tissues that were used for pathological diagnoses. The following monoclonal or polyclonal primary antibodies were utilized: CASP3 (1:100, Abcam, UK), TRAIL-R1 (1:100, Life Technology, USA), IGFBP (1:200, Santa Cruz Biotechnology, Germany), BAX (1:100, Santa Cruz Biotechnology), XAF1 (1:100, Santa Cruz Biotechnology), survivin (1:100, Cell Signaling Technology, USA), ERK (1:75, Cell Signaling Technology), RAF1 (1:100, Santa Cruz Biotechnology), BCL2 (1:100, Santa Cruz Biotechnology), MDM2 (1:100, Santa Cruz Biotechnology), MLL2 (1:100, Santa Cruz Biotechnology), RIZ (1:50, Santa Cruz Biotechnology), EZH1 (1:200, Abcam), NSD2 (1:50, Abcam), KDM5c (1:100, Abcam), JMJD2a (1:200, Abcam), UTX (1:100, Santa Cruz Biotechnology), and JMJD5 (1:100, Abcam).
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2

Assessing OPC Survival with PDE7-GSK3 Inhibitors

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Purified OPCs were placed on coverslips coated with poly-L-lysine (Sigma) and laminin (Engelbreth-Holm-Swarm murine sarcoma; Sigma; 2 × 104 cells/well) and they were cultured with dual PDE7-GSK3 or GSK3 inhibitors (VP3.15 or TDZD8; 1 μM) in a previously described serum-free differentiation medium78 (link), consisting of BME:F12 (1:1; Invitrogen) supplemented with 100 μg/ml transferring (Sigma), 20 μg/ml putrescine (Sigma), 12.8 ng/ml progesterone (Sigma), 10.4 ng/ml sodium selenite (Sigma), 25 μg/ml insulin (Sigma), 0.8 μg/ml thyroxine (Sigma), 0.6% glucose (Normapur), 6.6 mM glutamine (Invitrogen) and 100 U/mL penicillin, 0.1 mg/ml streptomycin and 0.25 μg/ml Amphotericin B antibiotic anti-mycotic solution (Sigma). After 2 DIV, they were fixed with 4% paraformaldehyde (PFA) and subjected to immunocytochemistry for active caspase 3 (Casp3; 1:200; Abcam; Cat#ab13847) and the OPC marker A2B5 (1:10; Hybridoma Bank). 10–20 microphotographs from each coverslip were taken randomly with an In Cell Analyzer 1000 (GE-HealthCare) and the number of Casp3+-A2B5+ double positive cells was counted using the software In Cell Analyzer 1000 Workstation (GE-HealthCare). Data were expressed as a mean ratio of double positive cells for Casp3 and A2B5 with respect to the total number of A2B5+ cells ± SEM for each condition in at least three independent experiments.
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3

Cryosectioning and Immunohistochemistry for Retinal Analysis

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For cryosection analyses, heads or enucleated eyes were fixed in 4% (w/v) PFA in PBS for up to 2 h on ice. The tissues were equilibrated overnight at 4°C in 30% (w/v) sucrose in PBS and embedded in OCT compound (Sakura Finetek). Flat-mount dissections were done as described above for lineage tracing. Immunohistochemistry was performed on cryosections (10 µm) or flat-mount retina as previously described (Cantrup et al., 2012 (link); Ma et al., 2007 (link)). An additional blocking step involving M.O.M Blocking Reagent (Vector Labs) was used in all experiments involving monoclonal primary antibodies. The following primary antibodies and dilutions were used: BrdUAlexa555 (1:20, BD Pharmingen, #560210); Brn3 (1:50, SCBT, #sc6026); Casp3 (1:500, Abcam, #ab13847); NEFH, (1:1000, Covance, #SMI31R); PH3 (1:100, Millipore, #06-570); pS6S235/236 (1:200, Cell Signaling Technology, #4857); pS6S240/244 (1:200, Cell Signaling Technology, #5364). All immunohistochemistry antibodies have been independently verified in our previous studies (Hagglund et al., 2017 (link); Jones et al., 2015 (link)).
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4

Chondrocyte Protein Extraction and Analysis

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Passage 2–3 chondrocytes were used for protein extraction. The method for collagen type II (COL2A1) extraction was as described previously [27 (link)]. Briefly, chondrocytes were washed with PBS three times and lysed with RIPA lysis buffer (Beyotime, China) supplemented with 1 mM protease inhibitor cocktail and 1 mM phosphatase inhibitor cocktail (Thermo, USA). The mixture was homogenized and lysed on ice and centrifuged at 12000 r/min for 30 min, 4 °C. The resulting supernatant was collected. Protein concentration was determined by the BCA method. The same amount of protein sample was electrophoresed and transferred to the polyvinylidene fluoride (PVDF) membrane (Millipore, USA). The membrane was blocked with 5% skim milk for 1 h at room temperature, and incubated at 4 °C overnight with the primary antibody against COL2A1 (Abcam, UK), MMP-13 (Abcam, UK), CGRP (GeneTex, USA), iNOS (GeneTex, USA), COL1A1 (Abcam, UK), TGFβ1 (Abcam, UK), PCNA (Abcam, UK), Casp3 (Abcam, UK), and GAPDH (Abclonal, USA). After washing, the membrane was incubated with the secondary antibodies (Abcam, UK) at room temperature for 1 h. Integrated density for protein bands was determined using Tanon 5200 (Tanon Science &Technology, China).
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5

Isolation and Analysis of Exosomes

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ExoQuick-TC exosome-isolation reagent (EXOTC50A-1), SeraMir exosome RNA-isolation kit (RA808A-1), exosome-specific marker anti-αCD63 antibody (EXOABCD63A-1), and florescence exosome-preparation reagent (EXDC300A-1) were from System Biosciences (SBI, Palo Alto, CA, USA). Penicillin-streptomycin (PS) solution, trypsin-EDTA solution, RPMI medium, and α-MEM media were obtained from Life Technologies GIBCO (Grand Island, NY, USA). Fetal bovine serum (FBS) was from Sigma-Aldrich (St. Louis, MO, USA). Antibodies used for immunoblotting were against phosphorylated p53 (Cell Signaling Technology, Beverly, MA, USA), BAX, BCL2, CASP9, CASP3, β-actin (Abcam, Cambridge, MA), and cytochrome c (ENZO Diagnostics Inc., Farmingdale, NY, USA).
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6

Immunohistochemical Analysis of Cellular Markers

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After incubating with 10% FBS, the sections were incubated with primary antibodies overnight at 4°C, then, the primary antibodies were replaced by secondary antibody labels and cell nuclei were stained with DAPI. Primary antibodies: α-SMA (cat. no. Ab5694; dilution: 1:50; Abcam), CASP3 (cat. no. ab32351; dilution: 1:50; Abcam), IL-1β (cat. no. ab254360; dilution: 1:50; Abcam). Secondary antibodies: Alexa Fluor® 568-conjugated goat anti-rabbit immunoglobulin G (cat. no. A-11034; dilution, 1:250; Thermo Fisher Scientific), and Alexa Fluor® 488-conjugated goat anti-mouse immunoglobulin G (cat. no. A32727; dilution, 1:250; Thermo Fisher Scientific). Images were obtained by E2000U microscope (Nikon Corporation, Tokyo, Japan).
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7

Western Blot Analysis of Myocardial Proteins

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The proteins lysed from left ventricle were separated by 10% SDS-polyacrylamide gel and transferred to PVDF membranes using a semidry transferring method. The membranes were sharked for 1 h and incubated with specific primary antibodies at 4°C overnight. The next day, the membranes were incubated in horseradish peroxidase- (HRP-) labeled secondary antibodies (Beyotime, Nanjing, China), colored with fluorescent substrates and captured on the Bio-Rad system. Antibodies against collagen I, collagen III, p-P65, Bcl-2, Bax, CASP-3, GAPDH, and histone H3 were purchased from Abcam (Cambridge, MA, USA). Antibodies against p-ERK, p-JNK, p-P38, TGF-β1, α-SMA, MMP9, and TIMP-1 were obtained from Cell Signaling Technology (Danvers, MA, USA). GAPDH and histone H3 were used as internal controls.
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8

Histological Analysis of Spinal Cord Injury

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For histological analysis, the spinal cord specimens were managed the same as above reported. Immunofluorescent staining was performed on 20‐μm sections, which were stained with the following antibodies: green fluorescence protein (GFP, 1:200, A10262, Molecular probes); neurofilament (NF, 1:200, Ab8135, Abcam); caspase 3 (Casp3, 1:200, Abcam); neuron‐specific marker (NeuN, 1:200, Ab104224, Abcam), ß‐tubulin III (Tubulin; 1:100, T8578, Sigma); glial fibrillary acidic protein (GFAP, 1:400, Ab10062, Abcam); oligodendrocyte‐specific antibody (O4, 1:200, Ab7474, Abcam); and 4′,6‐diamidino‐2‐phenylindole (DAPI, 1:1000, D1306, Invitrogen). Sections of spinal cord were imaged at 10×, 20×, and 40× magnifications using a confocal microscope (Leica SP5, Germany). GFP staining was performed to check the survival of the BMSCs. NF staining was used to detect axon growth in the injured area. NeuN staining was performed to detect the spared neurons in the area adjacent to the lesion. Double immunofluorescent assay (GFP/Tubulin, GFP/GFAP, GFP/O4) was performed to determine whether the GFP+ cells (include the BMSCs) differentiate into other types of cell.
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9

Keratinocyte stress response via immunocytochemistry

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Primary keratinocytes were seeded in a 12-well plate at 100,000 cells/well in LabTek Chambered -Microscopic slides (Thermofisher, Australia) and exposed to UV and/or heat stress. For immunocytochemistry, cells were fixed with 4% paraformaldehyde, washed twice with TBS. Skin tissues were processed and stained according to previous protocols [14 (link)]. Primary NHEK and skin sections were incubated with antibodies to either thymine dimer (CPD) (mouse monoclonal, 1:500 dilution; Kamiya Biomedical, USA), p53 antibody (rabbit monoclonal 1:50 dilution; Abcam, USA), p53 acetyl K382 (rabbit monoclonal 1:200, Abcam USA), SIRT1, SIRT1-p, Casp-3 (cleaved), Survivin or anti-pan Cytokeratin and ki67 (rabbit polyclonal, 1:50 dilution; Abcam, USA). The mouse monoclonal antibody to pan-cytokeratin (1:50; Abcam, USA) was used to label keratinocytes. The secondary antibodies anti-mouse Alexa Fluor 488 (for keratin and CPD) and anti-rabbit Alexa Fluor 550 (for caspase 3, p53 and ki67) were used for detection. Three sections were analysed per exposure replicate and five images of randomly selected fields-of-view were captured from each section. To determine percentages of keratinocytes positive for each individual antibody, positive cells were quantified within 5 images randomly chosen per section.
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10

Immunofluorescence Staining of Cell Markers

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Sections were immersed in a preheated antigen unmasking solution (Vector, H-3300) in a microwave oven at 95°C for 15–20 minutes, followed by cooling at room temperature for 20 minutes and incubation with a blocking reagent (PerkinElmer, FP1012) for 1 hour and then a primary antibody overnight at 4°C. The following primary antibodies were used in our study: active Caspase-3 (Casp3; Abcam, ab2302; 1:100), phospho-Histone H3 (pH3; Millipore, 06–570; 1:100), non-muscle myosin heavy chain IIA (NMHCIIA; Biolegend, 909801; 1:500), phospho-Smad2 (pSmad2; Cell Signaling, 3108; 1:500), phospho-Smad1/5/9 (pSmad1/5/9; Cell Signaling, 13820; 1:500), ΔNp63 (p63; Biolegend, 619002; 1:100), Sox2 (Abcam, ab97959; 1:1000), Sox2 (Santa Cruz, sc-17320; 1:100), and SSEA1 (Developmental Studies Hybridoma Bank, AB 528475; 1:10). After three washes in PBS, sections were incubated with the Alexa Fluor 568 or Alexa Fluor 488 (1:200, Invitrogen) secondary antibody for 2 hours at room temperature. For pSmad2 and pSmad1/5/9, HRP-labeled goat anti-rabbit IgG (PerkinElmer, NEF812001EA; 1:200) was used as secondary antibody and a TSA kit was used for signal detection (PerkinElmer, NEL741001KT). Sections were counterstained with DAPI (Sigma, D9542). Images were captured using a fluorescence microscope (Leica DMI 3000B) with filter settings for DAPI/FITC/TRITC.
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