Inflammobiota TrialC_HiSeq-8
"DNA and RNA were extracted with a phenol-chloroform bead-beating procedure (Griffiths et al 2000) and kit purification (Qiagen AllPrep DNA/RNA Mini kit). Total RNA was reverse-transcribed using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) with modifications as described before (Berry et al. 2011). cDNA libraries were paired end sequenced using a Illumina GenomeAnalyzer or a HiSeq (CSF Vienna). Read pairs were overlapped using FLASH (Magoc and Salzberg, 2011). Metatranscriptomic sequencing data were analyzed following the double RNA analysis pipeline described by Urich et al. (Urich et al 2008). proportions rRNA/mRNA. Briefly, rRNA tags were taxonomically-binned using MEGAN (Huson et al 200X, Urich et al 2008). mRNA tags were compared against the NCBI non-redundant database using BlastX and taxonomically-classified using MEGAN. SEED categories were assigned using the MG-RAST Server (Version 2, significance threshold: E-value 10-5) (Meyer et al 2008)"