Table 10

Experimental design and values for ChIP replicates and input samples

Experiment #

Experiment ID

Barcode

Sample

DNA Concentration (ng/φL)

A260/280

Total reads

Mapped reads

% Mapping

Threshold


1

PolII_Rep1

ACGT

PolII

16.6

1.83

1110177

623328

56.15

14

2

Input_CATT

CATT

Input

51.6

1.85

2526689

1719855

68.07

Not being scored

3

Cse4_Rep1

GTAT

Cse4

12.0

1.99

2606497

1080537

41.46

81

4

Ste12_Rep1

TGCT

Ste12

11.6

1.85

2020432

1072428

53.08

42

5

Input_ACGT

ACGT

Input

66.9

1.80

4678579

2857615

61.08

Not being scored

6

Cse4_Rep2

CATT

Cse4

8.6

1.85

679315

357384

52.61

25

7

Ste12_Rep2

GTAT

Ste12

9.4

1.86

2316023

1067739

46.10

44

8

PolII_Rep2

TGCT

PolII

15.5

2.00

3991833

2561147

64.16

12

9

PolII_Rep3

ACGT

PolII

9.7

1.97

2661304

1725793

64.85

42

10

Input_NB

None

Input

60.4

1.83

2432221

1582226

65.05

Not being scored

11A*

Cse4_Rep3

None

Cse4

10.7

1.69

1168583

239580

20.50

60

11B*

Cse4_Rep3

None

Cse4

10.7

1.69

3245287

583876

17.99

12A*

Ste12_Rep3

None

Ste12

9.1

1.64

2106917

473965

22.50

39

12B*

Ste12_Rep3

None

Ste12

9.1

1.64

2668067

551040

20.65

13

PolII_Rep4

None

PolII

18.8

1.94

4649077

3151068

67.78

40

14

Input_NB

None

Input

60.4

1.83

4373256

2455181

56.14

Not being scored

15

Input_ACGT

ACGT

Input

66.9

1.80

873037

529038

60.60

5

16

Input_CATT

CATT

Input

51.6

1.85

799430

479546

59.99

5

17

Input_GTAT

GTAT

Input

34.6

1.69

1380820

850262

61.58

6

18

Input_TGCT

TGCT

Input

68.1

1.78

611123

362458

59.31

4


NB (No Barcode) indicates that standard non-barcoded Illumina adapters were used. DNA concentrations of Illumina DNA libraries and their A260/280 ratios are given in columns 5 and 6.

Mapping values after sequencing (total sequencing reads, total mapped reads and percentage of mapped reads) are shown in columns 7, 8 and 9.

Threshold values for PeakSeq scoring algorithm are displayed in column 10.

* Sample ran twice on sequencer and reads pooled together from both lanes for scoring as a single experiment

Lefrançois et al. BMC Genomics 2009 10:37   doi:10.1186/1471-2164-10-37

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