Root specific silencing-related and nitrogen-dependent small RNA profiling of Arabidopsis ProAtUBQ10:AtAMT1;1-ORF transgenic plants(R4N Sample, from roots under normal hydroponics conditions)
The constitutive expression of ammonium transporter (AMT) AtAMT1;1 under a atamt1;1-1 (ko11) mutant background of Arabidopsis thaliana showed higher transcript level in shoots under nitrogen starvation and degradation in roots. Whether the nitrogen- and organ- dependent expression of AtAMT1;1 is regulated by small RNAs remains unknown. To identify potential silencing-related small RNAs, we first compared small RNA profiles between a stable ProAtUBQ10:AtAMT1;1 transgene and the silencing 35S:AtAMT1;1 transgene in ko11 background roots. Total RNA was extracted from 6-week-old hydroponic grown  transgenic plants by TRIzol reagent (Invitrogen) following the manufacturer’s instructions. Small RNA libraries were constructed using TruSeq Small RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Gel slices corresponding to approximately 15–30 nt smRNAs were recovered and then sequenced by Illunina HiSeq2000 platform at Novogene Bioinformatics Institute.