Extended Data Fig. 7: Pairing bias of high confidence m6A sites and false positive sites in HEK293T and mESCs.
From: Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library
a) Predicted RNA structures of two synthetic oligos (RNA6 and RNA7) with ACA motif located near stem region. The RNA structures are predicted by Vienna package. b) Gel imaging of two synthetic oligos after MazF cleavage. An oligo (RB1) completely cleaved is also shown as positive control. c) Increasing the amount of MazF does not improve the digestion efficiency for oligo RNA7. Sequences of synthetic oligos are provided in Supplementary Table 22. Assays of MazF digestion on synthetic oligo had conducted once. d) Pairing bias for high confidence m6A sites and false positive sites. Coordinate 0 indicates the location of interested sites. Pairing probabilities of upstream and downstream 25 bp flanking sequencing are calculated in respect to the high confidence m6A sites, false-positive sites and random sampling sites. Pairing bias = log2(Pair_probfalse (i,j)/Pair_probrandom (i,j)), where Pair_prob(i,j) is the mean pairing probability of bases between position i and position j. Red color indicates the RNA fragments are more likely to form pairing than random sites.
