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13 protocols using mef2d

1

Hindbrain, Retina, and Tumor Immunohistochemistry

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Hindbrains and retinas were processed as described (del Toro et al. 2010 (link); Pitulescu et al. 2010 (link); Fantin et al. 2013 (link)), and tumors and E10 embryos were fixed in 4% PFA for 1 h on ice. After incubation in blocking solution (10% normal donkey serum, 0.1% [v/v] Triton X-100 in PBS), samples were incubated overnight at 4°C with the designated primary antibodies (MEF2A [Abcam], MEF2B [Abcam], MEF2C [Cell Signaling], MEF2D [BD], EP300 [Active Motif], HDAC4 [GeneTex], DLL4 [R&D Systems] isolectin B4 [IB4] [Vector Laboratories], and Erg [Abcam]) in 0.1% PBS-T. Samples were washed in PBS-T and incubated for 3 h with suitable species-specific Alexa fluor- or biotin-conjugated secondary antibodies in 0.1% PBS-T. Total numbers of branch points and tip cells and retinal outgrowth length were measured after IB4 staining using ImageJ software from pooled images of retinas from at least two independent litters.
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2

Histone Deacetylase Inhibitor Screening

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The primary antibodies used were anti: MEF2D (BD Bioscience); MEF2A (C-21), (Santa Cruz Biotechnology); MEF2C (15 (link)); Actin (Sigma-Aldrich); HDAC4 (16 (link)); HDAC5 (17 (link)); HDAC7 (18 (link)); HDAC9 (19 (link)); H3K27ac (ab4729) and H3K9ac (ab4441) (Abcam); Histone H3 (H0164, Sigma-Aldrich) HDAC3 (PA5-29026, Invitrogen). The following chemicals were used: SAHA (Cayman Chemicals); TMP195 (MedChemExpress), BML-210 (Sigma-Aldrich). The PAOA derivatives MC2983, MC2984, MC2985 and MC2991 were synthetized. All new compounds had spectral (1H NMR, ESI-MS) data in agreement with the structure. Full details of the syntheses will be reported elsewhere. NKL54 (N-(2-aminophenyl)-N'-[3-(trifluoromethyl)phenyl]heptanediamide) was synthesized by SIA Chemspace (Riga, Latvia).
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3

Immunofluorescence Staining of Mef2D in ASM Cells

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Mouse ASM cells were fixed in 3.7% formaldehyde and permeabilized with 0.5% Triton X-100 in phosphate-buffered saline (PBS) for 5 min. Cells were blocked with 10% normal goat serum in PBS for 1 hour at room temperature and incubated overnight at 4°C with primary antibody Mef2D (1:500; BD Biosciences) in 10% normal goat serum. Cells were washed three times with PBS for 10 min and incubated with secondary antibodies conjugated to fluorescein isothiocyanate (1:200; Invitrogen) in 10% normal goat serum for 2 hours at room temperature. Cells were washed three times with PBS and stained with DAPI (Sigma-Aldrich) for 15 min at room temperature. Cells were washed three times with PBS, and images were captured using a Zeiss LSM confocal microscope (Carl Zeiss).
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4

Immunoblotting and Immunofluorescence Protocol

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Rabbit polyclonal MEF2A antibody was produced with the assistance of the York University (Toronto, ON, Canada) Animal Care Facility. MEF2D (BD Biosciences, Mississauga, ON, Canada, 610775), KLF6 (Santa Cruz, Dallas, TX, USA, R-173 and E-10), Actin (Santa Cruz, sc-1616), IRDye 680RD goat anti-rabbit (LI-COR, Bioscience, Lincoln, NE, USA) and IRDye 680RD goat anti-mouse (LI-COR, Bioscience) were used for Immunoblotting experiments. FITC- and TRITC-conjugated α-rabbit and α-mouse secondary antibodies and 4,6-diamidino-2-phenylindole (DAPI; D9542), H2O2 (H0904) and H89-dihydrochloride hydrate (B1427) were purchased from Sigma Aldrich (Toronto, ON, Canada). Atenolol (Sigma Aldrich, A7655), Isoproterenol hydrochloride (Sigma Aldrich, 1351005) and ICI 118551 hydrochloride (Abcam, Toronto, ON, Canada, ab1200808) were purchased for use in cell culture.
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5

Western Blot Analysis of Myogenic Markers

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C2C12 mouse myoblasts or human myoblast cell HSMMs were washed with PBS and lysed in RIPA buffer [50 mM Tris-HCl, 150 mM NaCl, 1% NP 40, 0.1% SDS, 0.5% deoxycholate, Protease Inhibitor Cocktail (Roche)]. Total protein (~20 μg) was separated in SDS-PAGE, transferred to PVDF membranes and immunoblotted with specific antibodies; AKAP6 (1:3000, Covance PRB-451P), AKAP79 (1:3000, BD 610314), MEF2D (1:3000, BD 610774), MyHC (1:3000, Sigma M4276), MEF2C (1:3000, Cell signaling #9792), AKAP-Lbc (1:3000, Santa Cruz sc-9336), AKAP12 (1:3000, Santa Cruz sc-33578), MEF2A (1:3000, Santa Cruz sc-313), myogenin (1:3000, Santa Cruz sc-12732), MyoD (1:3000, Santa Cruz sc-760), actin (1:3000, Santa Cruz sc-1616), α-tubulin (1:5000, Calbiochem CP06). After incubation with horseradish peroxidase conjugated secondary antibody (1:5000, Santa Cruz sc-2005, sc-2004, sc-2020) for 1 h, immunoreactive bands were visualized with enhanced chemiluminescence with Novex® ECL Chemiluminescent Substrate Reagent (Invitrogen).
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6

Antibody Detection Assay for Epigenetic Markers

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Antibodies used were against MEF2D (BD Bioscience), H3K27ac (ab4729; Abcam, Cambridge, MA, USA). H3K27me3 (ab195477, Abcam) HDAC4 (Paroni et al., 2004), γH2AX (9718, Cell Signalling, Leiden, The Netherlands), TP53 (DO‐7; Dako, Santa Clara, CA, USA), LT SV40 (sc‐147, Santa Cruz), Lamin B1 (ab16048, Abcam), p21 (CP74, Sigma), RACK1 (sc‐17754, Santa Cruz, Dallas, TX, USA), GFP (Paroni et al., 2004).
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7

Antibodies and Chemicals Used in Cellular Assays

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The primary antibodies used were anti: MEF2D (BD Bioscience); MEF2A (C-21), Caspase-3 (E-8) and FAS (M-20) (Santa Cruz Biotechnology); RAN and Caspase 8 (D35G2) (Cell Signaling Technology); Actin, BrdU, and FLAG/M2 (Sigma-Aldrich); GFP, HDAC4 and Caspase-9 (15 ); HDAC5 (21 (link)); H3K27ac (ab4729) and H3K27me3 (ab6002) (Abcam); H3K4me3 (GTX128954, GeneTex). The anti-HDAC9 antibody was produced in rabbit by injecting a His-tagged fragment of HDAC9 (aa 275–600) expressed in Escherichia coli. The antiserum was affinity purified against the same fragment GST-tagged of HDAC9.
The following chemicals were used: Doxorubicin and Metformin (Alexis); Lapatinib and Imatinib (LC Laboratories); MKK2206 and SAHA (Cayman Chemicals); BrdU (Sigma-Aldrich); FasL (Peprotech).
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8

Antibody Validation for Protein Analyses

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The primary antibodies used were as follows: MEF2D (BD Biosciences, San Jose, CA, USA); MEF2A (C‐21 Santa Cruz Biotechnology, Dallas, TX, USA); p53 and pERK (Cell Signaling Technology, Leiden, the Netherlands); p21, Actin, anti‐BrdU, FLAG M2 and RACK‐1 (Sigma‐Aldrich); RAS (Abcam, Cambridge, MA, USA); GFP and HDAC4 (Paroni et al., 2004); and HDAC5 (Clocchiatti et al., 2015). Anti‐CD44‐FITC (BD Biosciences) and CD24‐APC (BioLegend, San Diego, CA, USA) were used with matched control antibodies, anti‐mouse IgG1 FITC and IgG2a APC (Miltenyi Biotec, Bergisch Gladbach, Germany). HDAC7 antibodies were generated in rabbits by injecting recombinant histidine‐tagged HDAC7 fragment aa 261–522. For anti‐HDAC7 antibody purification, HDAC7 was fused to glutathione S‐transferase and cross‐linked to glutathione‐Sepharose as described previously (Paroni et al., 2004).
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9

Antibody Validation for Protein Analysis

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Rabbit polyclonal MEF2A antibody has been previously described (34 (link)). The following antibodies were purchased from Santa Cruz: actin (sc-1616), dsRed (sc-33354), MEF2A (sc-313X; used in ChIP), donkey anti-goat IgG-horseradish peroxidase (IgG-HRP) (sc-2020), ERK-1 (sc-93). The following antibodies were obtained from Cell Signaling: p38 (9212), phospho-p38 (9211), phospho-ERK1/2 (4370). Myogenin (clone F5D) monoclonal antibody was provided by the Developmental Studies Hybridoma Bank (DSHB). Goat anti-Rabbit IgG-HRP (170–6515) and goat anti-mouse IgG-HRP (170–6516) were from Bio-Rad Laboratories. The remaining antibodies are as follows: MEF2D (BD Biosciences, 610775), DUSP6 (Abcam, ab76310), Rabbit IgG (Millipore, 12–370), IRDye 680RD goat anti-rabbit (LiCOR) and IRDye 680RD goat anti-mouse (LiCOR). SB 202474 (Santa Cruz) and SB 203580 (Cell Signaling) was used at a concentration of 5 μM.
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10

Western Blot Analysis of MEF2D Protein

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Cell protein was harvested with ice-cold lysis buffer containing protease inhibitors. Protein was separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and then the separated protein was transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore Corporation, Bedford, MA, USA). After 2-h blocking with 5% fat-extracted milk at room temperature, the membranes were incubated overnight at 4°C with primary antibodies against MEF2D (1:3,000; BD) and β-actin (1:4,000; Abcam). Then the membranes were washed with TBST three times and then were treated with horseradish peroxidase-conjugated secondary antibody for 2 h at room temperature. Protein bands were visualized by chemiluminescence detection.
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