RNA-Seq of Mus musculus: Bladder implanted with MB49 cell line with CIITAKO treated with BCG
For RNA sequencing, mouse bladders were implanted with GFP-expressing MB49 or MB49CIITAKO tumors and treated with weekly BCG or PBS. On Day 21, tumors were removed, and single-cell suspensions were prepared and stained with BUV395 anti-CD45 antibody. To select tumor cells, GFP-positive, BUV395-negative cells were sorted.Tumor cell RNA was prepared from fresh frozen cell pellet samples using QIAGEN RNeasy Mini Kit according to manufacturer instructions. After PicoGreen quantification and quality control by Agilent BioAnalyzer, equimolar libraries were pooled and run on a HiSeq 2500 in Rapid Mode, PE50, using the HiSeq Rapid SBS Kit - HS (Illumina). The loading concentration was 9.8 pM (2500) and spike-in of PhiX was added to the run to increase diversity and for quality control purposes.