GSM8528372: WT infected, sample 1; Mus musculus; RNA-Seq
Total RNA was extracted from samples using a RNeasy Micro Plus Kit (Qiagen). Total RNA integrity was determined using Agilent Bioanalyzer or 4200 TapeStation. Library preparation was performed with 10 ng total RNA with a Bioanalyzer RNA integrity number score greater than 8. Double standard complementary DNA (cDNA) was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, and cycles per burst 50 for 120 s. cDNA was blunt ended, had an A base added to the 3′ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 to 15 cycles using primers, incorporating unique dual index tags.