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Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer.
This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes.
Bisulfite sequencing was used for preliminary evaluation of DNA methylation in large regions of selected CpG islands in randomly selected patients.
It has been suggested that DNA pooling allows accurate assessment of average DNA methylation in large groups of individual genomes [ 46, 47].
Moreover, the stable nature of DNA compared with RNA and the availability of high-throughput techniques for measurement of DNA methylation in large sample sets add advantages for its clinical application.
We demonstrate that MMSDK is a genome-wide, high-throughput and cost-effective method to analyze DNA methylation in large genomes such as the human and that MMSDK can be used to reveal connections between genomic, epigenetic and transcriptional features.
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For the methylation status of DLEC1, we found a significantly higher level of DLEC1 methylation in large-sized tumors, which is consistent with a previous study [ 37].
Cigarette smoke is an established environmental associate of DNA methylation (12– 17) and maternal smoking in pregnancy has recently been found to be associated with levels of DNA methylation in large-scale epigenome wide association studies (EWAS) of cord blood (18) and infant whole blood shortly after delivery (19).
This optimized MSPCR protocol allows for a rapid determination of ACSL3 5'-CGI methylation status in large sample sets, which is a normal requirement in population studies.
The study has notable strengths including analyzing genome-wide gene specific DNA methylation in a large population of mothers.
We further investigated the OPCML-v1 promoter methylation in a large collection of primary tumors, some with corresponding normal tissues as controls (Fig. 6A and Table 1).
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