Alkaline Phosphatase, Calf Intestine-Tobacco Acid Pyrophosphatase Sequencing

CIP-TAP maps capped small RNAs (Gu et al., 2012). In this method, RNA is treated with CIP followed by 3′-end linker ligation. Next, the RNA is treated with TAP, followed by 5′-end linker ligation. The fragments are reverse-transcribed to cDNA, PCR-amplified, and sequenced. Deep sequencing provides single-nucleotide resolution reads of the capped small RNAs.


  • Identifies capped small RNAs missed by CapSeq
  • High throughput


  • Nonlinear PCR amplification can lead to biases affecting reproducibility
  • Amplification errors caused by polymerases


Illumina Library prep and Array Kit Selector


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Gu W., Lee H. C., Chaves D., et al. CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell. 2012;151:1488-1500