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63 protocols using dnmt3a

1

Western Blot Analysis of Apoptosis-Related Proteins

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NK92 cells or U937 cells were lysed using Laemmli lysis buffer (Sigma-Aldrich). Blots were prepared and then blocked with 5% dry milk solution in TBST for 1 h. Primary antibodies to HCA1, HAC2, HCA3, gasdermin-D, DNMT3A, DNMT3B or Caspase-1 (Abcam, Cambridge, UK) were used. HRP conjugated goat anti-rabbit or goat anti-mouse secondary antibodies (Cell Signaling Technology, Danvers, MA, USA), were diluted in fresh 5% dry milk in TBST solution and incubated with the blots for 1 h at room temperature. HRP was detected using BioRad ECL Western blotting detection reagent (BioRad, Hercules, CA, USA). Primary antibody for Actin (Cell Signaling Technology) was used to confirm loading equality.
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2

Western Blot Analysis of Mouse Tissue Proteins

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We homogenized mouse tissues in buffer containing 50 mM Tris–HCl (pH 8.0), 150 mM NaCl, 1% Nonidet P‐40, 0.5% deoxycholate, 0.1% SDS, and 1 mM 2‐mercaptoethanol with Halt Protease Inhibitor Cocktail (Thermo Fisher Scientific, NJ, USA) and then centrifuged them at 2,500 × g for 15 min. Equal amounts of protein were separated by 5–20% SDS–PAGE and transferred to Hybond‐P membranes (GE Healthcare, Piscataway, NJ, USA). The primary antibodies and their dilutions were as follows: AR (N20, 1:1,000; Santa Cruz Biotechnology, Santa Cruz, CA, USA), Dnmt1 (1:1,000; Abcam, Cambridge, MA, USA), Dnmt3a (1:1,000; Abcam), Dnmt3b (1:1,000; Abcam), Hes5 (1:1,000; Santa Cruz), and ChAT (1:1,000; Millipore, Billerica, MA, USA). Primary antibody binding was probed with horseradish peroxidase‐conjugated secondary antibodies at a dilution of 1:5,000, and bands were detected by using an immunoreaction enhancing solution (Can Get Signal; Toyobo, Osaka, Japan) and enhanced chemiluminescence (ECL Prime; GE Healthcare). An LAS‐3000 imaging system (Fujifilm, Tokyo, Japan) was used to produce digital images. The signal intensities of these independent blots were quantified using IMAGE GAUGE software version 4.22 (Fuji) and expressed in arbitrary units (n = 3 for each group). The membranes were reprobed, or the same samples were examined with an anti‐GAPDH (1:5,000; Santa Cruz) antibody for normalization.
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3

Western Blotting of EMT Markers

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Western blotting was performed according to standard procedures using enhanced chemiluminescence detection. Briefly, total proteins were extracted from cells using RIPA lysis buffer (Thermo Fisher Scientific). Equal amounts of protein were separated on sodium dodecyl sulfate–polyacrylamide gels and then polyvinylidene fluoride membrane (Millipore). After blocking with 5% skim milk, the membranes were incubated with the primary antibodies for DNMT3A, DNMT3B, E-cadherin, N-cadherin, vimentin and GAPDH (Abcam), followed by incubation with corresponding horseradish peroxidase-coupled secondary antibody (Beyotime). The signals were detected with enhanced chemiluminescence reagents (Pierce). GAPDH was used as an internal control.
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4

Western Blot Analysis of Protein Targets

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Western blots were performed as previously described [21] (link), using the following antibodies detecting: Akt (cat.# 4691, Cell signalling, dilution 1:1000), Dnmt1 (cat.# ab188453, Abcam; dilution 1:500), Dnmt3a (cat.# SC-20703, Santa Cruz; dilution 1:1000), Dnmt3b (cat.# PA1–884, Thermo Fisher; dilution 1:1000), Stat3 (cat.# SC-8019, Santa Cruz; dilution 1:500), P-Stat3 (cat.# 9145, Cell signalling, dilution 1:1000), Stat5 (cat.# 25656, Cell signalling, dilution 1:1000), P-Stat5 (cat.# 9359, Cell signalling, dilution 1:1000), mouse c-Met (cat.# SC-8057; Santa Cruz; dilution 1:500), c-Myc (cat.# SC-40, Santa Cruz; dilution 1:1000), Hsc-70 (cat.# SC-7298, Santa Cruz; dilution 1:10000), Lin28b (cat.# SC-293120, Santa Cruz; dilution 1:500), h-Ras (cat.# SC-520, Santa Cruz, dilution 1:1000) and β-actin (cat.# SC-130657, Santa Cruz; dilution 1:1000).
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5

Placental Protein Quantification by Western Blot

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Western blot analysis was performed as previously described22 (link). Placental samples were lysed in RIPA buffer in the presence of protease and phosphatase inhibitor cocktail (Pierce Biotechnology, Rockford, IL). Protein concentrations were determined by BCA assay (Pierce, Rockford, IL). Thirty µg of protein lysate was reduced (Dithiothreitol, DTT), and subjected to sodium dodecyl sulfated polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene fluoride (PVDF) membrane. The blots were incubated with antibodies specific for Acel-K27-His3, DNMT1, DNMT3a, PGC-1α (Abcam, Cambridge, MA), TFAM, P(S97)-ACC, or β-actin (Cell Signaling Technology, Danvers, MA), and detected by enhanced chemiluminescence (Pierce, Rockford, IL). The blots were quantified and analyzed by imaging densitometry with Image Lab Software (Bio-Rad, Hercules, CA).
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6

Western Blot Analysis of EMT and DNMT Markers

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The analysis of western blot was described previously [28 (link)]. Briefly, total protein was extracted and applied to SDS-polyacrylamide gels for electrophoresis (22 mA per gel). Protein was transferred onto 0.45 μm polyvinylidene difluoride (PVDF) membranes for 1.5 h with 400 mA. The transferred membranes were incubated with blocking buffers for 10 min and then incubated with specific primary antibody against E-cadherin (BD), N-cadherin (Genetex), Vimentin (BD), DNMT 1 (Abcam), DNMT 3A (Abcam), DNMT 3B (Cell signaling), or β-Actin (Cell signaling) at appropriate dilutions at 4 °C overnight. The membranes were washed and incubated with horseradish peroxidase-linked secondary antibody for 1 h at room temperature. Bands were visualization by chemiluminescent reagent and record by photographic film and the intensity of the band was quantified and calculated. The results were conducted independently in triplicate.
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7

Quantifying DNMT Protein Levels

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The level of DNMT proteins was determined by Western blot analysis using primary antibodies against DNMT1, DNMT3A, and DNMT3B (Abcam, Cambridge, MA, USA) as described in Tryndyak et al. [22 (link)]. Equal protein loading was confirmed by immunostaining against GAPDH (Abcam).
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8

ChIP-seq analysis of AML1, ETO, and epigenetic regulators

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Formaldehyde (1% final concentration) was added into cells (2 × 106 cells). Cells were then incubated for 10 min at 37°C to crosslink proteins to DNA. After sonication, 5 μg of antibodies recognizing the following AML1 (Santa Cruz Biotechnology, Santa Cruz, USA, sc-28679), ETO (Santa Cruz Biotechnology, Santa Cruz, USA, sc-9737), histone deacetylase 1 (HDAC1) (Abcam, Cambridge, USA, ab7028), DNA methyltransferase 1 (DNMT1) (Abcam, Cambridge, USA, ab13537), DNMT3a (Abcam, Cambridge, USA, ab13888) and DNMT3b (Abcam, Cambridge, USA, ab13604) were immunoprecipitated with the chromatin overnight. Chromatin immunoprecipitation (ChIP) was performed on the naked and sonicated DNA extracted from SKNO-1, SKNO-1-siA/E, U937, and U937-A/E cell lines and then assayed with the EZ-ChIP kit (Millipore, Billerica, MA, USA, 17-371) according to the instructions of the manufacturer. Genomic EYA4 upstream regions, which were close to the putative AML1-binding site, were amplified. Primers sequences are shown in Supplementary Table 1. GAPDH was used as a control for nonspecific precipitated sequences.
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9

Western Blot Analysis of DNA Methylation Enzymes

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30 μg of cell lysates were analyzed on 8% Tris-Glycine polyacrylamide gels (Invitrogen) and transferred to PVDF membrane using BioRad mini transfer apparatus for 1.5 hour at 50 V. Membrane was blocked with 5% milk for one hour in room temperature and probed with Rabbit polyclonal anti-DNMT1 (Abcam, 1:1000), DNMT3A (Abcam, 1:500), DNMT3B (Abcam, 1:500), β-actin (Abcam, 1:500), Tet1 antibody (Abcam, 1:1000) or mouse monoclonal anti-TET2 (Active Motif 1:500) for overnight at 4°C. This was followed by washes in PBST (0.5% Tween 20) and incubation in HRP-conjugated secondary antibodies (Cal Biochem). Blots were developed using ECL reagent (GE Healthcare).
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10

Transcriptional Regulation of miR-34a

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RIP assays were performed using a RIP RNA-binding protein immunoprecipitation kit (Millipore) according to the manufacturer’s instructions. Antibodies against PHB2 (Bethl, Montgomery, TX), HDAC1 (Bethl) and Dnmt3a (Abcam) were added into the cell lysates. Lnc34a was retrieved from the complexes and evaluated by RT-qPCR. ChIP was performed using a ChIP assay kit (Millipore) as described previously (4). Antibodies against acetylated histones H3 and H4 (Millipore) were used to evaluate histone modifications associated with the miR-34a promoter. Enrichment of miR-34a promoter fragments was quantified by RT-qPCR with the primers: 5'-CACCTGGTCCTCTTTCCTTT-3' and 5'- TCCTCCTTCCTGCTCGT -3'.
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