Table 1.

Comparison of ChIP-chip and ChIP-Seq

	ChIP-chip	ChIP-Seq
Resolution	Array-specific, generally 30–100bp	Single nucleotide
Coverage	Limited by sequences on the array; repetitive regions usually masked out	Limited only by alignability of reads to the genome; increases with read length; many repetitive regions can be covered
Cost	$400–$800 per array (1–6 million probes); multiple arrays may be needed for large genomes	$1000–$2000 per Illumina lane (6–15 million readsprior to alignment)
Source of platform noise	Cross-hybridization between probes and non-specific targets	Some GC-biasmay be present
Experimental design	Single- or double-channel, depending on platform	Single channel
Cost-effective cases	Large fraction enriched (broad binding), profiling of selected regions	Small fraction enriched (sharp binding), large genomes
Required amount of ChIP DNA	High (few μg)	Low (10–50 ng)
Dynamic range	Lower detection limit, saturation at high signal	Not limited
Amplification	More required	Less required; single molecule sequencing without amplification is available
Multiplexing	Not possible	Possible