CIP-TAP
CIP-TAP
CIP-TAP maps capped small RNAs. 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.
Pros:
- Identifies capped small RNAs missed by CAP-Seq
- High throughput
Cons:
- Non-linear PCR amplification can lead to biases affecting reproducibility
- Amplification errors caused by polymerases
- Tobacco Acid Pyrophosphatase (TAP)
- Calf Intestinal Phosphatase (CIP)
- APex Heat-Labile Alkaline Phosphatase