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For example, for inferring the presence of a distinct nucleosome at stringency level ≥0.0, four continuous probes should have enrichment value ≥0.0.
The regions were mapped for the nucleosomal coverage (at stringency ≥−1.0 as earlier calculated using custom script 1) using fourth custom script.
Eight of the 65 markers hybridized with single clones and could not be assembled into contigs or merged with other singletons at stringency 1e-10 (Additional file 3).
Slides were then washed at stringency: 2X – 0.1X buffer/0.05% Tween 20 at 37°C -55°C with or without 50%60%60% formamide.
DNA fragments were subsequently analysed using capillary electrophoresis, and physical map was built based on the number of shared fragments (with the same size and label) among clones at stringency cutoff 1e-75 to produce robust contigs.
The nucleosomal coverage was calculated at stringency ≥−1.0 as size of the chromosome (in bp) divided by the total region covered by nucleosomes (distinct + fuzzy) for all the five chromosomes of A. thaliana (see Additional file 2).
Similar(51)
This suggested that at stringencies between 10−6 and 10−10, the reduction in peaks and genes identified was reflecting a simple truncation of the number of calls rather than increasing, biologically relevant discrimination.
Slides were washed repeatedly at high stringency at 72°C and treated with 40 μg/ml RNAse A at 37°C to remove non-specifically bound probe.
The BESs with multiple hits (more than eight) at high stringency (at least 100 bp aligned contiguously) were identified as repeat sequences.
Nonspecifically bound probe was hydrolyzed with RNase A (20 μg/μL) and washed at high stringency at 55°C with 2× salt sodium citrate/50% formamide (Ferguson et al. 1999).
Hybridization was performed overnight at 50°C, washed at RT twice at low stringency for 5 min and then at 55°C twice at high stringency for 15 min and were detected as above.
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