GSM6253371: Clostridium saccharolyticum, no uric acid, replicate 1; [Clostridium] saccharolyticum WM1; RNA-Seq
Cells were then subjected to lysozyme digestion, Proteinase K digestion and mechanical disruption with a mixer mill (RETSCH MM400) at 4 °C, 25/s, for 30 min. RNA was then purified using RNeasy kit (Qiagen), followed by DNase digestion and second RNA purification step using the RNeasy kit (Qiagen). Ribosomal RNA was removed with the Ribo-Zero Bacteria kit (Illumina). The RNA-seq libraries were prepared using a TruSeq Stranded mRNAseq Sample Prep kit with each sample individually ligated with unique adapters (Illumina). The libraries were quantitated by qPCR, pooled, and sequenced on one lane for 101 cycles from one end of the fragments on a NovaSeq 6000 using a NovaSeq SP reagent kit. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina) and adaptors were removed from the 3' end of the reads. Read 1 aligns to the antisense strand and read 2 aligns to the sense strand.