GSM9100112: mrsa02_1; Mus musculus; RNA-Seq
MRSA-infected and uninfected mouse kidneys were homogenized in 1200 µl TRI Reagent using a Minilys tissue homogenizer with a mixture of Soil Grinding beads (SK38) and Hard Tissue Homogenizing beads (CK28). Homogenization was done at the highest speed (5000 rpm) for 1 minute, followed by 1 minute on ice, for a total of 3 cycles. After centrifugation, RNA was extracted from the supernatant using the Zymo Direct-zol RNA miniprep Plus kit, including on-column DNase I digestion. Stranded total RNA-sequencing was performed at the Indiana University Center for Medical Genomics Core. cDNA library preparation was carried out using the Illumina total RNA plus Microbiome kit (Ribo-Zero Plus Microbiome for rRNA removal). Pooled libraries were sequenced on a NovaSeq 6000 sequencer at a final concentration of 300 pM to obtain 150 bp paired-end sequencing. Due to the low proportion of bacterial reads in host tissues, approximately 150 million reads per library were generated.