title: RNAseq of Sulfolobus islandicus: SSV13 infected replicate 2
design: S. islandicus culure was grown to mid-log phase (OD600=0.20-0.24) in DTU medium. Cells were collected by pelleting and flash frozen in ethanol and dry ice. Total RNA was prepared with a QIAGEN RNeasy kit with on-column DNase treatment with the QIAGEN RNase-free DNase Set according to the manufacturing protocols. RNA was visualized by agarose gel electrophoresis and quantified with Qubit 2.0 fluorometer and QubitTM RNA BR Assay Kit (Thermo Fisher Scientific, USA). Samples were stored at -80 C before submitting to the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign (UIUC) for RNA sequencing (RNAseq). rRNA depletion was carried out with the RiboZero bacterial kit (Illumina, USA) and libraries were prepared with the TruSeq Stranded mRNAseq Sample Prep Kit (Illumina, USA). Libraries were quantified by qPCR and sequence on a NovaSeq600. Fastq files were generated and demultiplexed using bcl2fastq v2.20 conversion software (Illumina, USA). Reads were trimmed with Cutadapt, quality filtered using Sickle, and paired ends were interleaved.