Bioanalyzer rna 6000 nano reagent kit

All 15 samples were sequenced via Illumina HiSeq^® 2500 System (Illumina Australia and New Zealand, VIC, Australia). Before sequencing, samples were quality checked with the Bioanalyzer RNA 6000 nano reagent kit (Agilent); and Illumina libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to established protocols at the Australian Genome Research Facility (AGRF). The resulting libraries were checked again with the TapeStation DNA 1000 TapeScreen Assay (Agilent). Cluster generation was performed immediately before sequencing on a cBot with HiSeq^® PE Cluster Kit v4-cBot. The sequencing was conducted using a HiSeq^® SBS Kit on a HiSeq^® 2500, operating with HiSeq Control Software v2.2.68 and base-calling with Real Time Analysis (RTA) v1.18.66.3 (Illumina). Raw RNA-Seq short read data for all samples are freely available on NCBI under BioProject PRJNA482687.

Library preparation and sequencing was carried out at the Australian Genome Research Facility (AGRF). Upon arrival at the sequencing facility, the quality of the samples was checked using a Bioanalyzer RNA 6000 nano reagent kit (Agilent) and libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to established protocols. Final libraries were again checked using Tapestation DNA 1000 TapeScreen Assay (Agilent). Cluster generation was performed on a cBot with HiSeq PE Cluster Kit v4 - cBot and sequencing was done on a HiSeq 2500 using a HiSeq SBS Kit. The Hiseq 2500 was operating with HiSeq Control Software v2.2.68 and base-calling was performed with RTA v1.18.66.3. Samples in the second sequencing run were pooled and split across two lanes to reduce sequencing bias (Table 1).