Skip to main content

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.