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Table 1 Summary of the ChIP-chip and ChIP-seq profiles analyzed in this study

From: ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

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
  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.