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As the coverage is a function of the number of reads obtained for a given sample (see Table 3 for detailed per sample read and coverage statistics), data were normalized by dividing the coverage of each base by the mean coverage for that sample.
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Therefore the per sample and per genotype costs of MIP analysis decrease with the increasing number of samples (Table 2).
An overview of the >1% major haplogroups can be seen in Figure 2; detailed results per island sample are in Supporting Information Table S1 and Figure S1.
(See 5 for detailed sample descriptions).
Per-sample details can be found in Table S12, and in the Gene Expression Omnibus (see "Data Availability" below).
In BMIQ, the estimation of the initial thresholds proceeds in an automatic fashion on a per-sample basis: in detail, we use the estimated thresholds from the type1 distribution (which always gives an excellent fit, Supplementary Fig. S1) to then obtain type2-specific thresholds using a simple correction reflecting the difference in the modes between the type1 and type2 distributions.
Both endogenous and exogenous N7-methyl-G and O-methyl-dG were analyzed using sensitive LC-MS/MS methods employing selected reaction monitoring with detection limits of one N7-methyl-G/10 dG and one O-methyl-dG/10 dG per sample (for details, see Supporting Information).
Most of these articles (n = 35) detailed the number of samples per subtype and how many of these stained positively; results from all of these 35 with references are summarized in Figure 5A.
Table 2: Per sample (sample) and per genotype (genotype) costs.
(a d) Line profiles of all analyzed GBs per sample and (e h) CPD variation (ΔCPDGB), across the GBs extracted from the line profiles (see text for details).
Between 20 30 cells were analyzed per sample.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com