5'-triphosphate-end-enriched cDNA
Total RNA was subjected to two rounds of poly(A)  selection and treated with Terminator 5'-phosphate-dependent exonuclease. Next, the RNA was treated with RNA 5'-polyphosphatase and a 5' adapter with a BpuE I restriction site (5'-GCACCATATAACCGCTTCCrUrUrGrArG-3') was ligated to the available 5'-monophosphate ends. Following first strand cDNA synthesis as described above, double-starnded cDNA was generated with a BpuE I Primer (5'-GCACCATATAACCGCTTCCTTGAG-3') and Pfx DNA polymerase. DNA fragments larger than 100 bp were gel purified, digested with BpuE I in the presence of S-adenosylmethionine. The DNA was separated on an agarose gel and several gel segments spanning the ~130 bp size range were excised and processed for Illumina sequencing.