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Fig. 1 | Genome Biology

Fig. 1

From: FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Fig. 1

Effect of BrdU incorporation into DNA on nanopore sequencing current signal. a Scheme of sample preparation. F, forward strand; R, reverse strand. b Bioanalyzer size control of the samples, with Qubit yield indicated. pTYB21, linearized plasmid; water, primer extension in the absence of dTTP and BrdUTP; dTTP, primer extension using canonical dNTPs; BrdUTP, primer extension using BrdUTP instead of dTTP. c Example of a 30-bp sequence of the forward (F) strand (positions 1000–1029) with current distribution of 500 reads at each position. Upper panel: sample obtained using canonical dNTPs. Lower panel : dTTP was replaced by BrdUTP. Blue rectangles highlight some current shifts due to the presence of BrdU. BrdU did not induce a current shift at all thymidine sites. d Current distribution for the “GATAA” pentamer for the dTTP (top) and the BrdUTP (bottom) samples on the forward (F, modified strand, left) and the reverse (R, native strand, right) strands. e Principal component analysis using as inputs 1-kb-long current value sequences (positions 100–1100 on the reference plasmid sequence) from 1000 reads for dTTP (black) and BrdUTP (brown) samples (F strand). The first two components are represented. Only “pass” reads were used in c, d,and e

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