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

BMC Genomics

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.

ISSN: 1471-2164