Table 1

Summary of the ChIP-chip and ChIP-seq profiles analyzed in this study

ChIP-chip and ChIP-seq replicates


IP factor

E-0-4 h

E-12-16 h

E-16-20 h

E-20-24 h

chip

seq

chip

seq

chip

seq

chip

seq


CBP

3

1

---

---

3

1

3

1

H3K27Ac

3

1

3

1

3

1

3

1

H3K27Me3

3

1

3

1

3

1

3

1

H3K4Me1

3

1

3

1

3

1

3

1

H3K4Me3

3

1

3

1

3

1

3

1

H3K9Ac

3

1

3

1

3

1

3

1

H3K9Me3

3

1

3

1

3

1

3

1

PolII

3

1

3

1

3

1

3

1

INPUT

*

1

*

1

*

1

*

1


For each combination of developmental stage and IP factor, three biological samples were profiled by ChIP-chip, and one of these samples was independently profiled by ChIP-seq. Therefore we have three biological ChIP-chip/ChIP-chip replicates, and one technical ChIP-chip/ChIP-seq replicate pair for every biological condition. *Although no independent microarray profiles of input DNA were available, we extracted input DNA profiles from the input channel (of the two-channel microarray) for each ChIP-chip profile. We therefore have 31 × 3 = 93 INPUT-chip profiles in this collection, where all INPUT-chip profiles within each time point are technical replicates.

Ho et al. BMC Genomics 2011 12:134   doi:10.1186/1471-2164-12-134

Open Data