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Table 1 ChIP-seq and Input library sizes in the mouse embryonic fibroblast cells in the study of [ 38 ] and in the D. melanogaster in the modENCODE 3955 dataset

From: Is this the right normalization? A diagnostic tool for ChIP-seq normalization

Modification

Library size,

Library size, “-2”

% of library

 

bp

filtration, bp

used

CTCF [38]

15,995,367

14,378,395

90

H3K4me3 [38]

18,466,608

17,047,383

92

H3K27me3 [38]

12,594,070

11,802,201

94

H3K36me3-1 [38]

16,675,805

14,397,781

86

H3K36me3-5 [38]

20,189,813

17,194,818

85

H3K36me3-8 [38]

19,588,306

16,700,104

85

H3K36me3-pooled [38]

56,453,924

48,292,703

86

Input [38]

19,672,479

17,099,127

87

H3K27me3 (modENCODE,id 1820)

13, 273,869

12,946,455

97

Input (modENCODE,id 1815)

13,425,292

13,168,039

98

H3K27me3 (modENCODE,id 1957)

11,997,853

11,807,914

98

Input (modENCODE,id 1961)

15,685,299

15,402,582

98

H3K27me3-pooled(modENCODE, id 1820and 1957)

25,081,783

24,754,369

98

Input-pooled(modENCODE,id 1815 and 1961)

28,827,874

28,570,621

98

  1. Note the pooled samples where obtained by pooling filtered libraries and did not undergo to a further filtration step.