Illumina HiSeq 2000 sequencing; Direct RNA Sequencing of polyadenylated RNA & high-depth Illumina strand-specific, short read RNA-seq of a stably RNAi-silenced nuclear 5'-3' exonuclease XRN3 mutant line in Arabidopsis thaliana
Direct RNA Sequencing of polyadenylated RNA & high-depth Illumina strand-specific, short read RNA-seq of a stably RNAi-silenced nuclear 5'-3' exonuclease XRN3 mutant line in Arabidopsis thaliana
Seedlings were harvested 14 day A. thaliana Columbia-0 background  seeds were sown aseptically in MS10 plates and are then stratified for 2 days before they are transferred to growth room. Growth room set up is long days (16h light/8h dark), temperature 21deg C which gives 23deg C on the shelf when lights are on. Total RNA extracted with the RNAeasy kit from Nimblegen. ERCC spike-ins were added to the total RNA at a 1:100 dilution and the resulting total RNA + spike-in mixture was stored at -80°C in advance of library preparation. Libraries were prepared using Illumina Tru-seq ribo-minus plant strand-specific protocol including barcoding.
Experimental Factor: xrn3-8 mutant
genotype
Experimental Factor: total RNA
fraction
Experimental Factor: Helicos DRS seqencing (no cDNA conversion)
protocol