Table 1.

The table shows repeat contents in Quiescent ChIP/Stimulated input, Stimulated ChIP/Stimulated input, Stimulated ChIP/Quiescent input, and Quiescent ChIP/Quiescent input peaks identified by RepeatMasker. The values are percentages of the combined peak lengths for each of the 4 samples separately. It is noticeable that the percentage share of Alus in the Stimulated ChIP samples (second and fourth columns, top row) are between 2 to 4 folds higher than the expected 10% (approximately) content in the genomic sequence. A converse pattern of enrichment of prevalence of LINEs in Quiescent ChIP samples is seen (first and third columns, second row). The percentages of other types of sequences do not show such marked variability. The Alu and LINE values in the dagger-marked rows were subjected to statistical testing as shown in Table 2.

	Quiescent ChIP/Stimulated input	Stimulated ChIP/Stimulated input	Quiescent ChIP/Quiescent input	Stimulated ChIP/Quiescent input
† SINEs	7.27%	38.64%	11.52%	26.3%
† LINEs	39.04%	22.87%	34.1%	28.69%
Satellites	23.89%	16.74%	18.05%	17.61%
Simple repeats	8.75%	6.99%	13.88%	10.32%
LTR elements	0.91%	1.07%	0.71%	0.98%
Not Masked	19.82%	12.54%	21.53%	15.67%
Low Complexity repeats	0.05%	0.09%	0.04%	0.03%
DNA elements	0.23%	0.14%	0.05%	0.03%
Unclassified	0.04%	0.76%	0.12%	0.32%
Small RNA	0%	0.16%	0%	0.05%