Metatranscriptome_Winter_10weeks_Infected2
For RNA extraction 100 ul of intestinal mucus were mixed with 500 ul of TriReagent (Invitrogen) and microbes were lysed in microbial lysis tubes (Qiagen) using 1 cycle of 30 s at 6 m/s in a FastPrep homogenizer (MP Biomedicals). Total RNA was extracted using the MagMAXTM-96 for Microarrays total RNA isolation kit (Life Technologies, Carlsbad, CA, USA) following the manufacturers instructions. The quality and integrity of the isolated RNA was checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent, Santa Clara, CA, USA). After quality and integrity procedures, rRNA was removed using the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina Inc. San Diego, CA, USA). Then, Illumina RNA-seq libraries were prepared from 500 ng of total ribo-depleted RNA using the Illumina TruSeq Stranded Total RNA Library Prep Kit (Illumina Inc. San Diego, CA, USA) according to the manufacturers instructions.