small RNA libraries from transgenic Arabidopsis expressing amiR-LFy
The small RNA library was produced from 50-100 μg of total RNA from 35S:AtMIR390a-Lfy transgenic Arabidopsis as described (Carbonell et al. Plant Cell 24, 3613-3629, 2012), and was barcoded in the amplicon PCR reaction step using the indexed 3’PCR-i5 primer (5’-CAAGCAGAAGACGGCATACGATGGTAAATTGATGGTGCCTACAG-3’) and the standard 5’PCR primer (5’-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3’). This small RNA library was multiplexed with other small RNA libraries generated similarly.    Sequencing reads were parsed to identify library-specific barcode (TTACCA) and remove the 3’ adaptor sequence (5’-CTGTAGGCACCATCAATC-3’), and were collapsed to a unique set with read counts. Unique sequences were aligned to a database containing the sequence of AtMIR390a-Lfy amiRNA foldback using BOWTIE version 0.12.8 with settings that identified only perfect matches (-f -v 0 -a -S). Small RNA alignments were saved in Sequence Alignment/Map (SAM) format and were queried using SAMTOOLS version 0.1.19+.
35S:AtMIR390a-Lfy