Summary: Poorey et al
Supplemental Methods and Figures
Poorey et al. "RNA Synthesis Precision is Regulated by Preinitiation Complex Turnover"
ChIP Tiling Array Data
Raw array data (CEL files) or the intensity data of the treatment (ChIP sample)
and control (mock sample) were quantile normalized separately within replicate groups
and the median intensity was scaled to a common target of 100. To determine the size
and the significance of the difference between ChIP and mock sample data (signal
estimates and the p values) we applied a Wilcoxon Rank-Sum test to log transformed
PM-MM values, log2(max(PMi-MMi,1)), whose genomic coordinate i (i.e., central
position of 25mer PM/MM probe sequence) fell within a 500 bp (i.e., the ChIP
fragmentation size) sliding window. The Hodges-Leman estimator, which is the
estimator associated with the Wilcoxon Rank Sum test, was calculated along with -
10log10(p-value). This analysis was applied to the following datasets:
1. WT TBP occupancy: 3 replicates of myc-tagged TBP ChIP as treatment
and mock ChIP as control in WT cells.
2. mot1-42 TBP occupancy: 3 replicates of myc-tagged TBP ChIP as
treatment and mock ChIP as control in mot1-42 cells.
3. WT TFIIB occupancy: 2 replicates of TFIIB ChIP as treatment and mock
ChIP as control in WT cells.