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We thank Shirley Liu for providing the raw ChIP chip data and Bart Deplancke for interesting comments on the manuscript.
All raw chip data was scaled in GCOS to 150 to normalize signal intensities for inter-array comparisons.
Prior to processing raw ChIP material for deep sequencing, ChIP-PCR validation studies were employed.
CEL files with raw chip intensity data were analyzed for copy number alterations at specific loci previously reported to be associated with ependymoma using segmentation algorithm in Partek Genomics Suite (v6.6).
Thus, peak-motifs allow to build PWMs from a set of known binding sites, or to perform a de novo motif analysis using the raw ChIP data as an input.
Because of the loss of a few samples due to sample processing or raw chip data quality assurance, the actual number of chips that were statistically analyzed were (respectively) 10, 5, 4, and 5 for control rats on days 0, 10, 21, and 28; and 9, 2, and 8 for arthritic rats on days 10, 21, and 28.
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We also included a raw ChIP-seq signal track.
The raw ChIP-seq data around the three sites showed double-peak distributions.
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