2008
DOI: 10.1093/nar/gkn210
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A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms

Abstract: DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the… Show more

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Cited by 38 publications
(29 citation statements)
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“…Sequencing chromatograms were analyzed using ab1 Peak Reporter (ThermoFisher, Waltham, MA) to generate numerical peak height data. Methylation at individual cytosines was calculated using Mquant as previously described (Leakey et al, 2008).…”
Section: Methodsmentioning
confidence: 99%
“…Sequencing chromatograms were analyzed using ab1 Peak Reporter (ThermoFisher, Waltham, MA) to generate numerical peak height data. Methylation at individual cytosines was calculated using Mquant as previously described (Leakey et al, 2008).…”
Section: Methodsmentioning
confidence: 99%
“…The PCR products were purified and sequenced at the DNA sequencing facility of Heinrich-Heine University. DNA methylation was quantified by the Mquant method as described (33). The height of the thymine peak at a CpG dinucleotide was subtracted from the average signal of 10 surrounding thymine peaks to quantify DNA methylation at this site.…”
Section: Subcellular Fractionation Of Hscs By Differential Centrifugamentioning
confidence: 99%
“…Band densities were determined using Labworks image acquisition and analysis software (Ultra-violet Products, Ltd., Cambridge, UK). Percent methylation was calculated as the density ratio of the two methylated bands to the three total bands (15). To confirm CO-BRA results, PCR products for samples of interest were cloned into the PGEM-T vector (Promega), and approximately 20 clones of each individual sample were sequenced.…”
mentioning
confidence: 99%