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76853
SimpleDIP™ Methylated DNA IP (MeDIP) Kit

SimpleDIP™ Methylated DNA IP (MeDIP) Kit #76853

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FIGURE 1. DNA immunoprecipitations were performed with 1 μg of genomic DNA from NCCIT cells and either 10 μl of 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb #28692 or 10 μl of Rabbit (DA1E) mAb IgG XP® Isotype Control (DIP Formulated) using SimpleDIP™ Methylated DNA IP (MeDIP) Kit #76853. The enriched DNA was quantified by real-time PCR using human Aqp2 intron 5 primers, human TIMP3 promoter primers, SimpleDIP™ Human Testis-Specific H2B Promoter Primers, and SimpleChIP® Human GAPDH Exon 1 Primers #5516. The amount of immunoprecipitated DNA in each sample is represented as signal relative to the total amount of input DNA, which is equivalent to one.

FIGURE 2. DNA immunoprecipitations were performed with 1 μg of genomic DNA from mES cells and either 10 μl of 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb #28692 or 10 μl of Rabbit (DA1E) mAb IgG XP® Isotype Control (DIP Formulated) using SimpleDIP™ Methylated DNA IP (MeDIP) Kit #76853. The enriched DNA was quantified by real-time PCR using mouse Aqp2 exon 1 primers, SimpleDIP™ Mouse Intracisternal A-Particle LTR Primers, mouse Lamc3 exon 1 primers, and SimpleChIP® Mouse GAPDH Intron 2 Primers #8986. The amount of immunoprecipitated DNA in each sample is represented as signal relative to the total amount of input DNA, which is equivalent to one.

FIGURE 3. The specificity of 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb #28692 was determined by dot blot. The same sequence of a 387 base pair DNA fragment was generated by PCR using exclusively unmodified cytosine, 5-methylcytosine (5-mC), 5-hydroxymethylcytosine (5-hmC), 5-carboxylcytosine (5-caC), or 5-formylcytosine (5-fC). The respective DNA fragments were blotted onto a nylon membrane, UV cross-linked, and probed with 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb. The top panel shows the antibody only binding to the DNA fragment containing 5-mC, while the bottom panel shows the membrane stained with methylene blue.

FIGURE 4. The specificity of 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb #28692 was determined by an ELISA. The antibody was titrated against a single-stranded DNA oligo containing either unmodified cytosine or differentially modified cytosine (5-mC, 5-hmC, 5-caC, 5-fC). As shown in the graph, the antibody only binds to the oligo containing 5-mC.

FIGURE 5. The specificity of 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb #28692 was determined by MeDIP. DNA IPs were performed with genomic DNA prepared from mouse embryonic stem cells, spiked with control DNA containing either unmodified cytosine, 5-methylcytosine (5-mC), or 5-hydroxymethylcytosine (5-hmc). IPs were performed using 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb and the SimpleDIP™ Methylated DNA IP (MeDIP) Kit #76853. The enriched DNA was quantified by real-time PCR using primers specific to the spiked-in control DNA sequence. The amount of immunoprecipitated DNA in each sample is represented as signal relative to the total amount of input DNA, which is equivalent to one.

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Product Description

The SimpleDIP™ Methylated DNA IP (MeDIP) Kit provides enough reagents to perform up to 10 genomic DNA preparations and 10 IPs from mammalian cells and is optimized for 1 μg of genomic DNA per IP. The SimpleDIP™ protocol can be performed in as little as two days and can easily be scaled up or down for use with more or less cells. Cells are first lysed and genomic DNA is extracted and sonicated into small fragments (200-500 bp). DNA IPs are performed using 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb and ChIP-Grade Protein G Magnetic Beads. After elution from the beads, the DNA is purified using DNA purification spin columns provided in the kit. The enrichment of particular DNA sequences can be analyzed by a variety of methods including standard PCR, quantitative real-time PCR, or next-generation sequencing. The SimpleDIP™ 5-Methylcytosine DNA IP Kit provides a highly validated 5-mC monoclonal antibody to ensure specific and robust signal. The kit also contains human and mouse control primer sets to regions of the genome that contain 5-methylcytosine. Thus, the IP of genomic DNA with 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb will enrich for the sequences amplified by the control primer sets, while the IP with Rabbit (DA1E) mAb XP® Isotype Control (DIP Formulated) will not result in any enrichment.

Specificity / Sensitivity

The SimpleDIP™ Methylated DNA IP (MeDIP) Kit can be utilized to detect endogenous levels of 5-methylcytosine modifications in mammalian cells (see Figures 1 and 2). The 5-Methylcytosine (5-mC) (D3S2Z) Rabbit mAb has been validated for specificity using ELISA, dot blot, and MeDIP assays and shows high specificity for its target DNA modification (see Figures 3-5). Positive control primer sets are included for human testis-specific H2B (TSH2B) promoter and mouse intracisternal A-particle (IAP) LTR, two genomic loci known to be methylated in most cell types. The use of other species with the kit requires the design of additional control primer sets.

Background

DNA immunoprecipitation (DIP) is a technique that uses antibodies to immunoenrich for regions of the genome containing modified nucleotides. This assay was first used with a 5-methylcytosine antibody to identify differentially methylated sites within normal and transformed cells (1). Investigators can use the DIP assay to look at specific genomic loci or look across the entire genome by utilizing next-generation sequencing (NGS) (2). When performing the DIP assay, cells are first lysed and the nucleic acids are recovered using phenol-chloroform extraction and ethanol precipitation. RNA is then removed by RNase A digestion, and genomic DNA is isolated by a second round of phenol-chloroform extraction and ethanol precipitation. The resulting genomic DNA is then fragmented by either restriction enzyme digestion or sonication and subjected to immunoprecipitation (IP) using antibodies specific to the modified nucleotide. Any sequences containing the modified nucleotide will be enriched by the immunoselection process. After IP, the DNA is purified and Quantitative Real-Time PCR can be used to measure the amount of enrichment of a particular DNA sequence. Alternatively, the DIP assay can be combined with NGS to provide genome-wide analysis of a specific DNA modification.

  1. Weber, M. et al. (2005) Nat Genet 37, 853-62.
  2. Down, T.A. et al. (2008) Nat Biotechnol 26, 779-85.
For Research Use Only. Not For Use In Diagnostic Procedures.

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