Fig. 1.

Results of the damidseq_pipeline. (A) The gene eyeless (ey) (highlighted) is expressed in D. melanogaster laval neural stem cells (Southall et al., 2013) and previously published microarray DamID in these cells (i) shows RNA polymerase II occupancy (Southall et al., 2013). (B) Performing DamID-seq in the same cell type illustrates the high correlation between Dam-Pol II (i) and Dam alone (ii) in terms of RPM (read counts/million mapped reads). Taking the ratio of the two RPM-normalized datasets fails to show significant RNA pol II occupancy at ey (iii); however, processing via the damidseq_pipeline software successfully recovers the RNA pol II occupancy profile while minimizing background (iv). See Supplementary Methods for experimental details