title: RNA-Seq of mir2392 treated SHSY5Y cells
design: RNA was extracted from cell culture dishes using TRIZOL TM.  RNA (500ng) was used as input for the Ion Total RNA-Seq V2 workflow. Briefly, adapters are hybridized, and reversed transcribed.  Libraries are amplified with barcoded primers (denoted in sample number) and cleaned up using AmpureXL beads.  Library QC was performed using a Bioanalyzer nano DNA chip, and libraries multiplexed and seeded into a cloning PCR reaction on an OT2 (540 kit).  Templated sequencing beads were enriched and loaded onto a 540 Ion Torrent sequencing kit.  The chip was sequenced using the RNA-seq workflow.  Each library was sequenced on two sequencing runs. Unaligned bam files from the two runs were merged and converted to fastq using picard tools.  Data were aligned to Grch38 human reference using STAR 2 pass mode and analyzed using LIMMA.