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For the 148 intra-chromosomal conversions, the conversion frequency decreased with the physical distance between gene pairs along the chromosome.
We also computed the conversion frequency using the number of bases instead of paralogous pairs, shown in the red bars of Figure 10B.
Of the 256 total events, 38.3% were detected by criterion 2. To examine the conversion frequency, we first computed the fraction of paralogous sequence pairs showing conversion, displayed in the blue bars of Figure 10B.
We found that GOF18 cells retained this ability even after prolonged culture under feeder-free conditions in the presence of FGF2 and Activin A. The conversion frequency in 2i alone was extremely low, but was greatly increased by addition of LIF (Supplementary Figure S2A).
To assess a minimal coverage threshold to identify putative NCO GCs for the DH lines, we used the same allele frequency cutoffs as for the analysis of the tetrad samples and calculated the conversion frequency for a series of minimal coverage thresholds.
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Compiled results from ~20 such crosses conducted in parallel (Fig. 1f) reveal the same overall trend regarding the conversion
The number of colonies was counted and the conversion frequencies was determined by dividing the number of yeast colonies appearing on SD-Ade plates (ADE+phenotype) by the number of yeast colonies appearing on SD+Ade plates.
In addition to the conversion frequencies in the general paralogous sequences, we also analyzed the incidence of conversion in protein-coding exons (green bars in Figure 10B).
To increase the frequency of conversion, we subdivided the bacterial stock showing the highest conversion frequency into groups of 10 and then repeated plasmid DNA transfection and screening.
In this comparison based on the number of bases, the α-globin cluster again shows the highest conversion frequency, with 75.0% of its duplicated bases involved in conversions.
The highest conversion frequency was found in the phospholipase D (AK070203) gene family.
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