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Table 1 Sequencing and peak metrics for ENCODE Kaiso ChIP-seq datasets

From: ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes

  GM12878 K5621 A549 HepG2 HCT116 SK-N-SH
Unique reads, Rep1 16,619,899 26,444,144 34,298,781 12,992,054 20,455,526 20,984,176
Sole-Search peaks, Rep1 2,396 11,257 14,414 1,560 8,813 12,290
Median peak tag height Rep1 24 25 25 26 21 23
Unique reads, Rep2 14,307,805 19,111,076 34,105,543 18,274,016 4,305,814 10,093,008
Sole-Search peaks, Rep2 2,784 15,395 11,559 2,342 936 2,789
Median peak tag height, Rep2 21 21 23 25 19 21
40% overlap (reciprocal overlap) 96% (97%) 83% (92%) 85% (81%) 66% (71%) 98% (94%) 65% (81%)
Unique reads, merged Reps 30,621,961 44,860,842 67,432,203 31,180,904 24,667,177 30,833,060
Sole-Search peaks, merged Reps 12,543 18,651 42,862 2,529 12,325 22,172
Median peak tag height, merged 20 34 27 30 23 25
High-confidence peaks 1,648 3,082 7,658 757 902 2,675
Median peak tag height 34 28 30 44 78 37
IDR peaks 2,144 3,285 7,152 2,879 4,325 N/A2
  1. For each dataset, two biological replicates of Bowtie-aligned .bam files were downloaded from the UCSC genome browser, and peaks were called using Sole-Search. The replicate with the most Sole-Search-called peaks was truncated so that both replicates contained the same number of peaks. Replicates were then compared by ENCODE standards using the 40% overlap rule (overlap percentage shown). Also shown are peak metrics for high-confidence Kaiso peaks in each cell line.
  2. 1 In the K562 dataset, amplified genomic regions were discovered to contain numerous false peaks that were not all removed by the peak-calling program; these peaks were removed from the list of high-confidence K562 peaks (see Additional file 2: Figure S2). The removed peaks had very high peak tag numbers because the amplified regions were over-sequenced. As a result of removing these false positive peaks, the median peak tag height of the high-confidence peaks is lower than the median peak tag height of the merged peak set. 2 At the time of paper submission, IDR peaks had not been called for Kaiso in SK-N-SH.