GSM3883380: Salmonella RiboZero 1; Salmonella enterica subsp. enterica serovar Typhimurium; RNA-Seq
Cultures grown to an OD600 of 2 were mixed with 0.2 volumes of STOP solution (95% ethanol, 5% phenol) and RNA was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer's protocol Before library preparation, rRNA depletion was performed for samples 1-3 using either the RiboZero Kit bacteria according to the manufacturer's protocol (Illumina; samples 2 and 3) or the riboPOOL protocol described in Kim et al. 2019 (Efficient depletion of ribosomal RNA for RNA sequencing in planarians; sample 1). For the riboPOOL protocol, 1 µg of total RNA and 1 µl 100 µM Salmonella-specific riboPOOLs (siTOOLS) were used and the amount of Streptavidin beads was reduced to 80 µl per sample. Sequencing libraries were prepared by IMGM Laboratories, Martinsried, Germany