title: GSM7025715: icSHAPE-SINEB2 Whole Cell NAI-N3 biol rep 2; Homo sapiens; OTHER
library_construction_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) and digested with DNaseI to remove DNA contamination. For subcellular fractionation, the method described by Pandya-Jones and Black (2009) (PMID: 19656867), and for the extraction of nuclear fraction, protocol from Brugiolo et al. (2017) (PMID: 28977534) were followed. The fractionated RNA was further purified by RNeasy Mini Kit (Qiagen) and treated with DNaseI. Purified Total, cytoplasmi and nuclear RNA were ribo-depleted and used for icSHAPE library construction. icSHAPE library preparation protocol was followed (PMID:26766114). Briefly, ribo-depleted RNA was biotin-clicked, fragmented and end-repaired. Next, RNA was 3' end ligated followed by cDNA synthesis and circularization. Final library was PCR amplified.