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Table 3 Overview of example murine ESC dataset from King et al. [16]

From: Cogito: automated and generic comparison of annotated genomic intervals

 

Base technology

 

mRNA

ChIP

ChIP

ChIP

ChIP

RRBS

  

H3K4me1

H3K4me3

H3K27ac

H3K27me3

 

Condition

      

J1

1

1

1

1

2

2

TKO

1

1

1

1

2

2

TKO3a1

2

1

 

2

1

2

TKO3a2

2

1

1

2

1

2

TKO3b1

1

1

1

1

1

2

DKO

1

1

 

2

1

1

DKO3a1

1

1

 

1

1

1

DKO3a2

1

1

 

1

1

1

DKO3b1

1

1

 

1

1

1

  1. This dataset includes samples of up to 9 conditions (J1, TKO, TKO3a1, TKO3a2, TKO3b1, DKO, DKO3a1, DKO3a2, DKO3b1), which were processed with three different base technologies: gene expression by RNA-seq, transcription factor binding sites by ChIP-seq, and methylation status by RRBS
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BMC Bioinformatics

ISSN: 1471-2105

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