The controls read about increasing geographical mobility.
The initial flicking time of each group was considered as the control reading.
This approach subtracts the control reads and accounts for the effective library size as well.
When the number of control reads mapped in a window is quite large compared with the average depth of the control reads, the region is considered as a highly repetitive region, which may lead to the identification of false-positive peaks; threshold (iv) effectively filters out such peaks.
Since the measured value for CENH3 enrichment is determined not only by ChIP reads but also by the control reads used for normalization, we used two control data sets, one derived from total nucleosomes and another from randomly fragmented DNA.
The following parameters were changed from default settings: -fastMap, -minIdentity = 99, -maxIntron = 5, and -minScore = 30 (87% of the CENH3 reads and 82% of the control reads could be aligned with the much more stringent setting -minScore = 300).
If condition (1) is fulfilled, the spike-in can be performed without the need for multiplex sequencing in order to later separate the control reads from other library molecules.
The repeat regions are disproportionately heavily sequenced relative to their frequency, encompassing 14%, 89% and 75% of the control reads from NRC1, pNRC100 and pNRC200 respectively (Table 4., Figures 3A and 3B).
Absorbance was read in a plate reader Opsys MR 96-well plate reader (Dynex Technologies, Chantilly, VA, USA) at 450 nm, with the control reading at 570 nm.
Thereafter, the recording continued until a signal was detected that resembled the initial control reading whereupon a second compound was added.
