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18 protocols using ki 67

1

Nifuroxazide in vitro and in vivo assay protocol

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Nifuroxazide was purchased from (Xiyashiji Chemical Co., LTD, ChengDu, Sichuan, China). Purity (98%) was measured by high-performance liquid chromatograph analysis. For in vitro assays, nifuroxazide was prepared initially as a 20 mM stock solution in dimethyl sulfoxide (DMSO) and stored at −20 °C. Then the stock solution diluted in the relevant assay medium, and 0.1% DMSO served as a vehicle control. For in vivo studies, nifuroxazide was prepared in 40% (v/v) polyethylene glycol 400 containing 5% (v/v) propylene glycol and dosed at 0.1 ml/10 g of body weight.
MTT, DMSO and Hoechst 33258 were from Sigma Chemical Co. (St Louis, MO, USA). The primary antibodies against Stat3/P-Stat3Tyr705, MMP-2, -9 (MMP-2, MMP-9), CC-3, Bcl-2 and β-actin were purchased from Cell Signaling Technology (Beverly, MA, USA). FITC-CD11b, PE-Gr1 conjugated antibodies were obtained from BD Biosciences (San Diego, CA, USA). Mouse monoclonal anti Ki-67 was purchased from Merck-Millipore (Bill, MA, USA). The Annexin V-FITC Apoptosis Detection Kit was purchased from KeyGen Biotech (Nan-jing, China).
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2

Pterostilbene and NTCU in Cell Signaling

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The pterostilbene compound with a purity of 98% was obtained from Friedemann Schmidt Chemicals. The N-nitroso-tri-chloroethylurea, (NTCU) was purchased from Toronto Research Chemicals, Inc. The primary antibodies were purchased from different companies with cytokeratin 5/6 (Biobyrt United Kingdom, UK); Ki-67 (Merck, Germany); p21 and p27 Proteintech, United States); β-actin, caspase-3 and cyclin E2 and D1 (Cell Signalling Technology, United States).
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3

Quantifying Spheroid Cell Proliferation and Apoptosis

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Cells were harvested carefully to ensure they retained their spheroid structure, pellets were resuspended in HistoGel (Thermo Scientific, Waltham, Massachusetts, US), fixed with 4% PFA (VWR International, Radnor, Pennsylvania, US), and embedded in paraffin. Sections of 4 μm were stained with haematoxylin (Mayer’s, Sigma-Aldrich Chemie, St. Louis, Missouri, US) and eosin (Merck Chemicals GmbH, Darmstadt, Germany) or Ki-67 (Clone SP6, monoclonal rabbit IgG, Order-no. 275R-16, LOT-no. 0000075544, Cell Marque, Rocklin, California, US). After heat-induced antigen retrieval at pH 9, anti-Ki-67 (1:100) was incubated for 30 minutes. For quantification of apoptosis, TUNEL assay (ApopTag® Plus Peroxidase In Situ Apoptosis Kit, Merck Chemicals GmbH, Darmstadt, Germany) was performed according to the manufacturer’s manual. For each experiment, at least 5 fields of view (20× magnification) per dose were counted and only immunoreactivity in nuclei or apoptotic bodies was considered positive.
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4

Autophagy and Apoptosis Regulation in Cells

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MTT, crystal violet solution, PI, RNAse A and DAPI were purchased from Beijing Solarbio Science & Technology Co., Ltd. Western blotting reagents were obtained from Beyotime Institute of Biotechnology. An Annexin V/PI apoptosis detection kit was purchased from 7 Sea Biotech (http://www.7seapharmtech.com/).
Primary antibodies against the following proteins were purchased from Cell Signaling Technology, Inc. (CST): AKT (cat. no. 9272), phosphorylated (p)-AKT (Ser473; cat. no. 4060), mTOR (cat. no. 2983), p-mTOR (Ser2448; cat. no. 5536), p70S6K (cat. no. 9202), p-p70S6 kinase (p70S6K; Ser371; cat. no. 9208), eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1; cat. no. 9644), p-4E-BP1 (Thr37/46; cat. no. 2855), Beclin-1 (cat. no. 3495), p-Beclin-1 (Ser93; cat. no. 14717), Cyclin D1 (cat. no. 2978), Cyclin E1 (cat. no. 4129), cleaved caspase-3 (cat. no. 9664), autophagy related 5 (ATG5; cat. no. 9980) and GAPDH (cat. no. 5174). LC3-I/II (cat. no. ABC929) was purchased from Sigma-Aldrich (Merck KGaA) and ki67 (cat. no. ab15580) was obtained from Abcam. Secondary horseradish peroxidase-linked antibodies against rabbit (cat. no. 7074) and mouse (cat. no. 7076) were purchased from CST. Small interfering RNA (si)ATG5 was purchased from Shanghai GenePharma Co., Ltd., and Lipofectamine® 2000 was obtained from Thermo Fisher Scientific, Inc.
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5

Quantifying Cell Proliferation in Xenografted Zebrafish

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Xenografted zebrafish embryos were fixed with 4% paraformaldehyde. Samples were first dehydrated with methanol followed by a rehydration step and treated with 10 ug/ml proteinase K for 10 minutes at 37°C. Then cells were blocked and permeabilized with 1% BSA and 0.5% Triton X-100 in PBS before incubation with primary antibody Ki 67 (Merck Millipore, Amsterdam, Netherlands #AB9260; 1:200 in blocking buffer) in 4°C for 12 h. Samples then were washed with 5% Triton X-100-PBS, incubated with donkey anti rabbit IgG Alexa Fluor 647 (Invitrogene #A31572 1:200 in blocking buffer) at room temperature for 2 h. After washing with PBS, the embryos were analyzed the using confocal microscope SP5 STED (Leica, Rijswijk, Netherlands).
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6

Comprehensive Protein Analysis Techniques

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Cells were lysed in RIPA buffer (Sigma) with protease inhibitor (Roche) and phosphatase inhibitor (Santa Cruz Biotechnology) cocktails for Western blotting. For immunohistochemistry (IHC), tissues were either fixed in 4% paraformaldehyde (PFA) and sucrose cryoprotected in OCT or in formalin and embedded in paraffin (FFPE). For FFPE tissues, after de-paraffinization and re-hydration, tissue sections were subjected heat for antigen retrieval. PFA/OCT sections were not subjected to antigen retrieval. Both IHC and immunocytochemistry of cell lines were performed with Alexa Fluor-conjugated secondary antibodies (Life Technologies) on 4% PFA-fixed cells. Nuclei were counterstained by DAPI. Fluorophore signals were captured with a Zeiss microscope (AXIO Imager A1) mounted with a charge-coupled device camera (Retiga EXi QImaging), and the images captured by Image-pro plus 6.0. Western blots and immunofluorescence assays were performed using the following antibodies: p-ERK1/2 (T202/Y204), p-c-FOS (S32), p-FRA1 (S265), p-p38 MAPK (T180/Y182), p-HSP27 (S82), p-Histone H2A.X (S139), total ERK1/2, c-FOS, FRA1, FOSB, p21, AIF, PARG, BRCA1, GAPDH (Cell Signaling Technology), TUBULIN (Sigma), PARP1, BRAF (Santa Cruz), PAR (Enzo), and Ki-67 (EMD Millipore). Western blot quantification was performed using NIH ImageJ.
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7

Liver Tissue Immunohistochemistry and Immunofluorescence

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Paraformaldehyde solution was used to fix liver specimens for 24 h. Paraffin sections (4 μm thick) were deparaffinized and rehydrated, followed by antigen retrieval, and then the tissue sections were incubated with the corresponding primary antibodies at 4 °C overnight. The chromogenic reaction was performed using a DAB solution for IHC assays. Primary antibodies were BrdU (cat. 5292; CST), pH3S10 (cat. 06-570; Merck Millipore), and Ki67 (cat. ab16667; Abcam). For IF, primary antibodies were CK19 (cat. ab52625, Abcam), ALB (cat. 16475-1-AP, Proteintech), MDIG (cat. 12214-1-AP; Proteintech), Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa Fluor™ Plus 555 (cat. A32794, Thermo Fisher), iFluor® 430 Tyramide (cat. 45096, AATbio), iFluor® 488 Tyramide (cat. 11060, AATbio) were used. Visualization of immunofluorescence was observed with a confocal laser scanning microscope (Leica, DM-8).
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8

Quantifying Tumor Cell Proliferation in Mice

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Mouse subcutaneous tumors were collected following euthanasia. Subsequently, tissue sections (4-µm) were dewaxed with xylene (twice) for 10 min and hydrated using a descending alcohol series (100% twice, 90% twice, 75% twice) for 3 min at room temperature. Antigens were retrieved in a 95°C water bath for 20 min. Endogenous peroxidase activity was blocked using 3% hydrogen peroxide for 20 min at room temperature. After blocking with 5% BSA (Sigma-Aldrich; Merck KGaA), the sections were incubated with primary antibody (Ki-67, 1:200; cat. no. 9027S; Cell Signaling Technology, Inc.) at 4°C overnight. The next day, sections were incubated with secondary antibody (1:200; cat. no. ZDR-5306; OriGene Technologies Inc.) for 2 h at 37°C, followed treating with DAB Chromogen (1 drop of the DAB Chromogen per ml of substrate buffer; Dako; Agilent Technologies, Inc.) and hematoxylin (cat. no. C0107; Beyotime Institute of Biotechnology) for 2 min at room temperature. Finally, the slides were dehydrated and fixed by resin and observed with an Olympus inverted microscope (Olympus Corporation; magnification, ×200).
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9

Betulin's Effects on Protein Markers

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To analyze the effects of betulin (3) on various protein markers, 20,000 NCI-H460 cells were seeded in a 24-well plate with or without betulin. After 48 hours treatment, media was discarded and cells were carefully and thoroughly washed with PBS. Then cells were fixed with 4% paraformaldehyde for 15 minutes at room temperature. Again, wells were washed with PBS and 150 µL Triton X-100 was added to the wells for 10 minutes. Cells were incubated with blocking solution for 30 minutes in a humidified environment followed by addition of primary antibody (1:100 dilution in blocking solution) overnight at 4°C. The next day, cells were washed with PBS and respective secondary antibody (Thermo Fisher Scientific) was added to the wells for 1 hour. Finally, DAPI staining was done followed by observing expression of markers under fluorescent microscope at 10× magnification. The primary antibodies used against the markers include BCL-2L1 (Santa Cruz Biotechnology Inc., Dallas, TX, USA), Ki-67 (EMD Millipore, Billerica, MA, USA), caspase-3 (EMD Millipore), caspase-6 (EMD Millipore), caspase-8 (EMD Millipore), and osteopontin (Abcam, Cambridge, MA, USA).
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10

Immunohistochemical Analysis of Transgenic Brains

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The animals were terminally anesthetized with Mebunat (Orion, Finland) and perfused intracardially with 4% paraformaldehyde in PBS or sacrificed with CO2. Brains were removed, post-fixed with 4% paraformaldehyde in PBS followed by embedding in paraffin. All histological and immunoassays were carried out on 7–10 μm sagittal sections. Immunohistochemical and immunofluorescence stainings were described previously40 (link) and performed on a minimum of n = 3 of each genotype. COX/SDH activity analysis is described elsewhere38 (link). Images were acquired with either Zeiss AxioImager epifluorescent microscope or Zeiss LSM 780 confocal microscope. Primary antibodies were rabbit Calbindin (Abcam), GFAP (Millipore), ALDH1L1 (Abcam), cleaved Caspase 3 (Cell Signaling Technology), IBA1 (Wako), Olig2 (Merck Millipore), KI67 (Merck Millipore); mouse Nestin (Merck Millipore), SDHA (CII) (Abcam), NeuN (Chemion), GAD67 (Merck Millipore); Neurofilament Marker pan axonal cocktail (BioLegend); chicken MAP2 (Thermo Scientific); rat MBP (Nordic BioSite). Golgi staining was processed using the FD Rapid GolgiStain Kit (FD Neuro Technologies). Fluoro-Jade C was from Millipore. Morphometrical analysis of coronal 80-μm-thick sections was described in ref. 41 (link). For cell counting, images from mid-sagittal sections were taken from three to six mice per genotype.
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