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Methylation extent was calculated as the mean methylation across four positions in the LINE1 region and five positions in the Alu-Yb8 region.
Mean methylation across the 26,486 autosomal CpG loci was not significantly associated with the birth weight groups (see Supplemental Material, Table 1).
The clade with the most conserved elements had significantly higher mean methylation across LTRs than either of the two diverged clades (p = 0.040 and p = 0.017).
Array-based mean methylation across the 26,486 CpG loci did not differ by any of the in utero exposures explored.
Our analysis so far compares CGI + SS in terms of their mean methylation across a set of samples and does not take into account between-sample variations.
The mean methylation across all mice for all IAP insertions was 72.5% and no mouse deviated by more than 3% (range 71-74%), showing no statistical difference (p > 0.99) (Table 2).
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We observed that the raw average methylation across CpG sites was dependent on coverage and therefore calculated a coverage-weighted mean methylation for each CpG site.
Global LINE1 measure was evaluated by calculating the mean methylation level across the 4 LINE1 CpG loci.
Mean methylation levels across methylation subgroups for pattern 1 (A), pattern 2 (B), and pattern 3 (C) DMRs.
Many of the DMRs (41%) show little variability in DNA methylation within the population – we define these as very low range DMRs (less than 0.2 mean methylation difference across all strains) and low range (between 0.2 and 0.4 mean methylation difference across all strains).
Standard curves were generated from each set of methylation controls by taking the mean methylation level across the amplified region; 7 CpG sites from the rat controls, and 13 CpG sites from the mouse controls.
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