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11 protocols using mouse anti histone h3

1

Spinal Cord Injury Protein Analysis

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Western blot (WB) was performed according to a previous method (22 (link)). Briefly, after animals were anesthetized and decapitated, spinal cord tissues of the lesion site were removed and collected immediately on ice (8 (link)). Then, samples were homogenized and lysed in RIPA buffer containing protease and phosphatase inhibitors. After centrifuging at 12,000 rpm for 10 min at 4°C, protein concentrations were determined using a BCA Assay Kit (Beyotime). Equal amounts of protein lysate (20 μg) were separated by 10% SDS-PAGE electrophoresis, followed by transferring onto PVDF membranes. After blocking in 5% fresh-non-fat skim milk prepared in TBST for 2 h at room temperature, membranes were incubated with the appropriate primary antibodies at 4°C overnight. Then, membranes were incubated with corresponding HRP-conjugated secondary antibodies for 2 h at room temperature after washing with TBST. Finally, protein bands were visualized with chemiluminescent HRP Substrate (Thermo Fisher) under Western Lightning-ECL (Bio-Rad, USA). The following primary antibodies were used: mouse anti-Histone H3 (citrulline R2+ R8 +R17) (Abcam; 1:1000), rabbit anti-ZO-1 (Abcam, 1:5000), rabbit anti-occludin (Abcam, 1:5000), rabbit anti-transient receptor potential vanilloid type 4 (TRPV4) (Abcam; 1:1000), and mouse anti-GAPDH (Zen-bio, 1:5000).
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2

SDS-PAGE and Immunoblotting of Chromosomal Proteins

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Proteins were sonicated, boiled in sample buffer (1% SDS, 16.7 mM Tris–HCl pH 6.8, 5% sucrose, 0.67 mM EDTA, 10% B-Mercaptoethanol (v/v)) and resolved using SDS-PAGE [78 (link)] with 10–15% polyacrylamide gels and 8 M urea in the stacking gel for better resolution of chromosomal proteins (electrophoresis apparatus; BioRad). For gel staining, protein bands were visualized using InstantBlue (Expedeon). For immunoblotting, proteins were transferred to nitrocellulose membranes and blocked with 5% non-fat milk in PBS-0.1% Tween for 1–2 h.
Primary antibodies used for immunoblotting included rabbit anti-GgCENP-T (1 : 2000) [6 (link)], rabbit anti-GgNdc80 (1 : 2000) [43 (link)], mouse anti-GgINCENP (1 : 3) [79 (link)], mouse anti-Histone H3 (1 : 500; Abcam), rabbit anti-GgTopo IIalpha (1 : 500) [80 (link)], mouse anti-alpha Tubulin (1 : 2000; B512 Sigma) and anti-GgCyclin B2 [81 (link)]. When using the LI-COR Odyssey system, membranes probed with secondary antibodies (IRDye 800 CW/IRDye 680; LI-COR Biosciences) were washed for at least 45 min with 0.1% Tween in PBS and a final wash performed with PBS for 5 min. Median fluorescence intensities for individual protein bands were subsequently determined using a CCD scanner (Odyssey; LI-COR Biosciences).
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3

Western Blot Analysis of Apoptosis Regulators

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Western blot analysis was performed as previously described43 (link) using the following antibodies: mouse anti-NOXA, rat anti-BMF, rabbit anti-MCL-1 (Enzo Life Science, Farmingdale, NY, USA), mouse anti-BCL-2, rabbit anti-BAK (BD Biosciences), rabbit anti-caspase-3, rabbit anti-caspase-9, rabbit anti-BIM, mouse anti-PARP, rabbit-anti PUMA, rabbit-anti BCL-xL (Cell Signaling, Beverly, MA, USA), mouse anti-GAPDH (HyTest, Turku, Finland), rabbit anti-H3K4me2 (Diagenode, Liège, Belgium), rabbit anti-acetylated histone H3 (Merck Millipore, Darmstadt, Germany) and mouse anti-histone H3 (Abcam) or mouse anti-β-Actin (Sigma, Germany). Goat anti-mouse, goat anti-rabbit and goat anti-rat IgG conjugated to horseradish peroxidase (Santa Cruz Biotechnology, Santa Cruz, CA, USA) and enhanced chemiluminescence (Amersham Biosciences, Freiburg, Germany) or infrared dye-labeled secondary antibodies and infrared imaging (Odysee Imaging System, LI-COR Biosciences, Bad Homburg, Germany) were used for detection. For detection of histone modifications cells were lysed using RIPA buffer supplemented with Pierce Nuclease (Thermo Fisher, Waltham, MA, USA). Representative blots of at least two independent experiments are shown.
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4

Western Blot Analysis of Proteins

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Equal amounts of proteins were separated by SDS-PAGE and electrotransferred to nitrocellulose membrane (GE-Healthcare Europe, Milano, Italy). Membranes were probed with primary antibodies, listed in Supplementary Table S2, followed by incubation with appropriated horseradish peroxidase (HRP)-conjugated secondary antibodies (Bio-Rad). Proteins were detected with Clarity Western ECL substrate (Bio-Rad) and quantified by densitometry using analytic software (Image Lab; Bio-Rad; https://www.bio-rad.com/it-it/product/image-lab-software). Results were normalized with respect to densitometric value of mouse anti-β-actin (Santa Cruz Biotechnology) for total and cytosolic extracts and mouse anti-histone H3 (Abcam) for nuclear proteins43 (link),58 (link) and then expressed as fold of wild-type RAGE+/+LeptrDb+/+mice value.
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5

Neutrophil Extracellular Trap Visualization

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dHL60 cells or PMN were adhered on 14-mm round glass slides coated with PLL (Liangyi, Dalian, China) and stimulated using activated complement complex, as described above, then fixed overnight in 2.5% glutaraldehyde at 4°C. For staining, slides were washed three times in PBS and blocked with goat serum working buffer (Zhongshanjinqiao, Beijing, China) and 2% BSA in PBS for 1 h at room temperature (RT). Rabbit anti-elastase (1:300, Merck) and mouse anti-histone H3 (1:500, Abcam) were used as primary antibodies in PBS containing 2% BSA for 1 h at RT. After washing, slides were incubated with goat anti-rabbit DyLight 488 (KPL) and goat anti-mouse Alexa Fluor 594 (Thermo) at 1:1,000 for 1 h at room temperature. Slides were then stained with DAPI and visualized using a confocal laser scanning microscope camera (Leica).
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6

Investigating DNA Damage Response Mechanisms

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siRNAs were obtained from Dharmacon. HMCES: D-020333–01 5’-GCGAACAUCCUGUCACUUA, J-020333–19 5’-CGUAAUGGAGAAACGGUCA, and J020333–20 5’-ACCAACUGUCGUAGUGAUA. Smartpools were purchased from Dharmacon for REV3L, Rad18, USP1, SHPRH, BRCA1, and BRCA2. The following antibodies were used: rabbit anti-HMCES (Sigma, HPA044968); mouse anti-GAPDH (Millipore, MAB374); mouse anti-RPA32 (Abcam, ab2175); rabbit anti-Cyclin A (Santa Cruz, sc-751); mouse anti-PCNA (Santa Cruz, sc-56); mouse anti-Histone H3 (Abcam, ab10799); mouse anti-FLAG M2 (Sigma, F3165); 5-methylcytosine (Abcam, ab10805); 5-hydroxymethylcytosine (Abcam, ab106918); ssDNA antibody (Millipore, MAB3034); mouse anti-p21 (Cell Signaling, 2946); mouse anti-p53 (Santa Cruz, sc-126); mouse anti-53BP1 (Millipore, MAB3802).
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7

Protein Quantification in Drosophila Brains

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Third instar larval brains were dissected in ice-cold 1xPBS. Samples were stored in 2x NuPAGE LDS Buffer at −20°C until use. After a round of sonication and treatment with DTT, samples were subjected to SDS-PAGE and transferred to a PVDF membrane for immunoblotting. Membranes were incubated with primary antibodies at 4°C overnight, washed and incubated with secondary antibodies at room temperature for 30min. Mouse anti-histone H3,1:2000 (Abcam #24834); rabbit anti-H3K4me3 1:2000 (Active Motif #39159); mouse anti-HA, 1:500 (Cell Signaling #2367S); rabbit anti-KDM5, 1:250 (Secombe et al., 2007 (link)); anti-gamma-tubulin, 1:1000 (4D11; Invitrogen MA1-850); and mouse anti alpha-Tubulin, 1:10000 (12G10, Developmental Studies Hybridoma Bank, University of Iowa) were used as primary antibodies. IRDye® 800CW Donkey anti-Rabbit IgG (92632213) and IRDye® 680RD Donkey anti-Mouse IgG (925-68072) from LI-COR were used as secondary antibodies. Western blots were quantified using LI-COR Image Studio software.
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8

Western Blot Quantification Protocol

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Through SDS-PAGE we separated equal amounts of proteins and electrotransferred to nitrocellulose membrane (GE-Healthcare Europe, Milano, Italy). After, membranes were probed with primary antibodies, listed in Supplementary Table 2, followed by incubation with appropriated horseradish peroxidase (HRP)-conjugated secondary antibodies (Bio-Rad). The detection of proteins was obtained with Clarity Western ECL substrate (Bio-Rad) and quantified by densitometric analysis software (Quantity-One; Bio-Rad). Results were normalized with respect to densitometric value of mouse anti-β-actin (Santa Cruz Biotechnology) for total and cytosolic extracts and mouse anti-histone H3 (Abcam) for nuclear proteins and then expressed as fold of control mice value.
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9

Protein Quantification in Drosophila Brains

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Third instar larval brains were dissected in ice-cold 1xPBS. Samples were stored in 2x NuPAGE LDS Buffer at −20°C until use. After a round of sonication and treatment with DTT, samples were subjected to SDS-PAGE and transferred to a PVDF membrane for immunoblotting. Membranes were incubated with primary antibodies at 4°C overnight, washed and incubated with secondary antibodies at room temperature for 30min. Mouse anti-histone H3,1:2000 (Abcam #24834); rabbit anti-H3K4me3 1:2000 (Active Motif #39159); mouse anti-HA, 1:500 (Cell Signaling #2367S); rabbit anti-KDM5, 1:250 (Secombe et al., 2007 (link)); anti-gamma-tubulin, 1:1000 (4D11; Invitrogen MA1-850); and mouse anti alpha-Tubulin, 1:10000 (12G10, Developmental Studies Hybridoma Bank, University of Iowa) were used as primary antibodies. IRDye® 800CW Donkey anti-Rabbit IgG (92632213) and IRDye® 680RD Donkey anti-Mouse IgG (925-68072) from LI-COR were used as secondary antibodies. Western blots were quantified using LI-COR Image Studio software.
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10

Antibody Dilutions for Western Blot

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Antibodies were used at the following dilutions: mouse anti-GFP antibodies (1:2000) and anti-HA-Peroxidase (1:5000) were purchased from Roche. Rat anti-AGO2 monoclonal antibody (1:200), rat anti-AGO1 monoclonal antibody (1:10) and rat anti-TNRC6B antibody (1:20) were kindly provided by G. Meister. Rabbit anti-DIS3L2 (1:1000) is a gift from A. Dziembowski and rabbit anti-STARPAP (TUT1) was kindly provided by R.A. Anderson and used at 1:3300. Rabbit anti-DIS3 (1:1000), rabbit anti-TUT7 (1:500), mouse anti-tubulin (1:5000), anti-mouse, anti-rat and anti-rabbit secondary antibodies (1:10000) were purchased from Sigma-Aldrich. Rabbit anti-XRN2 (1:500), anti-EXOSC3 (1:500), anti-RRP6 (1:3000) and mouse anti-Histone H3 (1:5000) were purchased from Abcam. Rabbit anti-XRN1 (1:2000) is from Bethyl laboratories.
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