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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 1000ā€“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 ā€œGATAAā€ 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 100ā€“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 ā€œpassā€ reads were used in c, d,and e

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