The largest database of trusted experimental protocols

6 protocols using dnmt1

1

DNMT1 Enrichment in MEG3 Promoter

Check if the same lab product or an alternative is used in the 5 most similar protocols
DNMT1 enrichment in MEG3 promoter region was analyzed using ChIP kit (Millipore, USA). When the MDA-MB-231 cells reached 70–80% in confluence, 1% formaldehyde was added and cells were fixed for 10 min. Later, the cross-linked products were randomly fragmented of appropriate size by 10 s of ultrasonication for 15 cycles with an interval of 10 s. After centrifugation at 13,000 rpm at 4 ℃, the collected supernatant was transferred into 3 tubes and cultured with positive control antibody RNA polymerase II, negative control antibody IgG of normal mice (Abcam, UK) and methylation transferase specific antibody DNMT1 (Abcam, UK) overnight at 4 ℃, respectively. Protein Agarose/Sepharose was applied to precipitate endogenous DNA–protein complexes, and the supernatant was adsorbed after a short centrifugation. The non-specific complexes were washed and de-crosslinked overnight at 65 ℃. Phenol/chloroform was used to extract and purify DNA fragments. qRT-PCR was used to test combination of DNMT1 and MEG3 promoter region. Primer sequences were detailed in Additional file 1.
+ Open protocol
+ Expand
2

ChIP Assay with Histone3 and LSD1

Check if the same lab product or an alternative is used in the 5 most similar protocols
The EZ-Magna ChIP kit (EMD Millipore) was used to conduct the chromatin immunoprecipitation (ChIP) assays in accordance with the manufacturer’s protocol. After carrying out the above-mentioned cell treatments, the cells were lysed with Cell Lysis Buffer and Nuclear Lysis Buffer and sonicated to obtain chromatin fragments. Next, the lysates were immunoprecipitated with Magnetic Protein A Beads conjugated with Histone3 (Millipore) or IgG (Millipore) as a control. Western blot assay was performed to detect the enrichment of LSD1, H3K27me1 (Millipore), H3K4me2 (Millipore), and DNMT1 (Millipore) in the precipitated protein complex.
+ Open protocol
+ Expand
3

Chromatin Immunoprecipitation (ChIP) Assay

Check if the same lab product or an alternative is used in the 5 most similar protocols
The ChIP assays were performed using EZ-Magna CHIP KIT according to the manufacturer’s instruction (Millipore, Billerica, MA, USA). SGC7901 and BGC823 cells were treated with formaldehyde and incubated for 10 min to generate DNA–protein cross-links. Cell lysates were then sonicated to generate chromatin fragments of 200–300 bp and immunoprecipitated with DNMT1 (Millipore) or the negative control IgG (Millipore). Anti-AcH3 (Millipore) was used as the positive control for the CHIP procedure. Precipitated chromatin DNA was recovered and analyzed by qRT-PCR (Additional file 1: Table S1).
+ Open protocol
+ Expand
4

Western Blot Profiling of Epigenetic Regulators

Check if the same lab product or an alternative is used in the 5 most similar protocols
Isolated cell pellets were lysed in RIPA buffer (Pierce, 89900) with 1X protease and phosphatase inhibitor (Pierce, A32961). Lysates were sonicated in a Bioruptor™ (Diagenode, Denville, NJ, USA) on ice for 8 minutes (8 cycles of 30 s on, 30 s off). Protein concentration was determined using a Pierce BCA Protein Assay Kit (Thermo Fisher Scientific, 23225) according to the manufacturer’s protocol. Samples were mixed with NuPAGE LDS 4x loading gel (NP0007) and NuPAGE 10x reducing agent (NP0009), and boiled at 95 °C. Next, samples were loaded onto 4–20% (BioRad, 4561093) or 10% gels (BioRad, 4561033) and transferred to LF PVDF (BioRad, 170–4274). Membranes were blocked with LI-COR Biosciences (Lincoln, Nebraska, USA) Odyssey Blocking Buffer (927–40100) or 5% milk-PBS-Tween. Bands were detected using Azure Biosystems (Dublin, California, USA) Imaging System c600. The antibodies used for immunoblotting included: DNMT1 (Sigma, D4692), PD-L1 (ProSci, 4059), HDAC1 (Cell Signaling, 2062), HDAC2 (Cell Signaling, 2540), HDAC6 (Assay Biotech, C0026), acetyl-alpha Tubulin (Cell Signaling, 3971), alpha-Tubulin (Cell Signaling, 3873).
+ Open protocol
+ Expand
5

Immunofluorescence Imaging of DNA Damage

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cells were seeded onto Lab-Tek II eight-well chamber slides (Thermo Fisher Scientific) and treated with the appropriate agents before washing in warm PBS. Cells were then fixed using 4% Paraformaldehyde (Life Technologies 28906) for 10 min at room temperature. Fixed cells were then washed in PBS and permeabilized in 0.1% Triton-X. Cells were washed in PBS prior to blocking for 1 h at room temperature with shaking in blocking buffer (0.1% Tween-20 + 5% FCS) then incubated with the appropriate primary antibody (DNMT1 (SigmaAldrich D4567) used 1:100, BRCA1 phospho S1423 (Abcam ab47325) used at 1 μg/ml and γH2A.X [3F2] (Abcam ab22551) used at 3 μg/ml) overnight at 4°C. After washing each chamber in blocking buffer, the corresponding secondary antibody was added, the chamber slide wrapped in foil and incubated at room temperature for 1 h. Each well was then washed with PBS. The chamber apparatus was removed and DAPI/Fluroshield (Abcam ab104139) was added to the slide. After coverslipping and sealing, slides were stored in the dark at 4°C prior to imaging. Images were captured on the Andor Spinning Disk Confocal Microscope. FITC was captured at an exposure time of 200 ms, Alexa Fluor at 100 ms and DAPI at 100 ms.
+ Open protocol
+ Expand
6

Chromatin Fractionation for Nuclear Protein Extraction

Check if the same lab product or an alternative is used in the 5 most similar protocols
CSC or control (DMSO treated) cells were collected at the indicated time points. To prepare nuclear extracts, cell pellets were were lysed in CEBN buffer (10 mM HEPES [pH 7.8], 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 0.2 % NP-40, 1X protease inhibitor cocktail (Invitrogen), 1X phosphatase Inhibitor cocktail, N-ethylmaleimide (Sigma) and Pefabloc SC AEBSF (Roche Applied Science)) and pellets were washed with CEB buffer (CEBN buffer without NP-40). For preparation of total nuclear protein extracts, nuclear pellets were lysed with 4% SDS and passed through QIAshredder (Qiagen). For preparation of Tight Chromatin fractions, nuclear pellets obtained after washing with CEB buffer, were further washed with soluble nuclear buffer (3 mM EDTA, 0.2 mM EGTA, inhibitors as described above), salt buffer with 0.45M NaCl concentration (50 mM Tris pH 8.0, 0.05% NP40, 0.45M NaCl). The pellet was then lysed in 4% SDS buffer using a QIAshredder column (Qiagen) and referred to as tight chromatin. Western blots of the protein extracts were probed with DNMT1 (Sigma), EZH2 XP (Cell Signaling), SIRT1 (Delta Biolabs), Lamin B (Santacruz Biotechnology). Band densitometry for western blots were quantitated using ImageJ software.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!