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. Author manuscript; available in PMC: 2011 May 1.
Published in final edited form as: Nat Rev Genet. 2010 Dec 30;12(2):87–98. doi: 10.1038/nrg2934

Table 1.

Next generation sequencing-based approaches for transcription start site mapping

TSS method RNA sequence data starting RNA Refs
CAGE 5′ end of transcripts 50 μg total RNA 9
DeepCAGE 5′ end of transcripts 10 ng total RNA 10
nanoCAGE 5′ end of transcripts 10 ng total RNA 12
CAGEscan 5′ end of transcripts and either 3′ end or internal RNA sequence 10 ng total RNA 12
PEAT 5′ end of transcripts paired with random reads along the RNA 150 μg total RNA 11

CAGE, cap analysis of gene expression; CAGEscan, paired read to combine 5′ CAGE with downstream sequence; DeepCAGE, high-throughput CAGE sequencing; nanoCAGE, low-quantity CAGE; ng, nanograms; PEAT, paired end analysis of transcription start sites; TSS, transcription start site.