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Methylated DNA immunoprecipitation (MeDIP or mDIP) is a large-scale (chromosome- or genome-wide) purification technique in molecular biology that is used to enrich for methylated DNA sequences. It consists of isolating methylated DNA fragments via an antibody raised against 5-methylcytosine (5mC).
Bayesian tool for methylation analysis, also known as BATMAN, is a statistical tool for analysing methylated DNA immunoprecipitation (MeDIP) profiles. It can be applied to large datasets generated using either oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq), providing a quantitative estimation of absolute methylation state in a region of interest.
Alternative methods to bisulfite sequencing include Combined Bisulphite Restriction Analysis and methylated DNA immunoprecipitation (MeDIP). Methodologies to analyze bisulfite-treated DNA are continuously being developed. To summarize these rapidly evolving methodologies, numerous review articles have been written. [2] [3] [4] [5]
A real-time polymerase chain reaction (real-time PCR, or qPCR when used quantitatively) is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR). It monitors the amplification of a targeted DNA molecule during the PCR (i.e., in real time), not at its end, as in conventional PCR.
In this article, RT-PCR will denote Reverse Transcription PCR. Combined RT-PCR and qPCR are routinely used for analysis of gene expression and quantification of viral RNA in research and clinical settings. The close association between RT-PCR and qPCR has led to metonymic use of the term qPCR to mean RT-PCR.
Bisulfite methods, such as used by RRBS, were also found more accurate than enrichment based, such as MeDip-Seq. [7] The data obtained on RRBS and the Illumina Infinium methylation are highly comparable, with a Pearson correlation of 0.92. [7] The data for both platforms are also directly comparable as both use an absolute measurement of DNA.
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