Total RNA, purified from the homogenate using the manufacturer's instruction, was treated with DNAse, followed by a phenol chloroform extraction.
Total RNA extracted from 5 × 10 by using Trizol reagent (Life Technologies Italia, Monza MB, Italy) according to the manufacturer's instruction was treated with DNase I (Invitrogen, VWR International, Milan, Italy) for 30 min at 37 °C.
Total RNA was isolated from 30 mg tissue samples using the Nucleospin RNA II kit (Macherey Nagel, Germany) as per manufacturer's instructions and was treated with DNase I provided within the kit.
Total RNA from HeLa cells, HeLa NE, and mouse tissues was extracted using Trizol (Invitrogen) according to the manufacturer's instructions and was treated with DNase I (Fermentas).
Total RNA was extracted from whole zebrafish larvae and different zebrafish tissues at several ages using the TRIzol Reagent (Invitrogen), following the manufacturer's instructions, and was treated with DNase I Amplification grade (1 unit/μg RNA, Invitrogen).
Total RNA was isolated from cultured cells using Trizol reagent (GBICOL/BRL, Gaithersburg, MD, USA) according to the manufacturer's instructions, and was treated with DNase I (Sigma-Aldrich, St . Louis MO) at 25°C for 15 min to minimize contamination by genomic DNA.
Total RNA was isolated from both embryonic and postnatal tissues using TRIzol Reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions and was treated with DNase I (Roche Applied Science, Penzberg, Upper Bavaria, Germany) to avoid genomic DNA contamination.
After resuspension and lysis (according to manufacturer's instructions), the material was treated with 800 µg/ml proteinase K for 1 h to 2 h at 55°C.
Total RNA was isolated using TRIzol Reagent (Invitrogen, Burlington, ON) from the pelleted cells following manufacturer's instructions, and it was treated with Deoxyribonuclease I (Invitrogen).
Arabidopsis thaliana (Col-0) leaves from 5 to 6 week old plants were used to prepare protoplasts as previously described [ 38] and genomic DNA and total RNA using Qiagen DNeasy and RNeasy plant kits (Qiagen, Melbourne VIC, Australia) following the manufacturer's instructions except total RNA was treated with Ambion DNase (Life Technologies, Melbourne VIC, Australia).
From this step forward, the supernatant was treated following the Qiagen instructions.
