Table 1.

Comparison of Microarray and RNA-Sequencing (RNA-Seq) for Studying the Transcriptome.

Technology	Microarray	RNA-Seq
Basis	Hybridization	High-throughput sequencing
Resolution	From several to hundreds of bases	Single-base
Required amount of input RNA	Nanograms (ng) to micrograms (μg)	Picograms (pg) to nanograms (ng)
High throughput	Yes	Yes
Reliance on reference sequence	Yes	Not necessarily
Ability to multiplex	No	Yes
Background noise	High	Low
Dynamic range	100-folds	>9000-folds
Splicing isoform detection	Limited to custom-designed microarrays	Yes
Allelic expression	Limited to custom-designed microarrays	Yes