|
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.
