title: RNA-seq of Mus Musculus: microglia
design: RNA samples were amplified using the Single Primer Isothermal Amplification (SPIA)Ovation RNA Seq System kit (Nugen). Double stranded cDNA was monitored foramplification using the Bioanalyzer High Sensitivity kit (Agilent) and samples withsignificant amplification were sheared and used as input for the Ion Xpress Plus HiQ gDNAFragment Library Preparation kit (Life Technologies). Bead preparation, emulsion PCR, andenrichment of DNA samples were performed with the Ion DNA Library Express v2 or HiQkit on the Ion OneTouch 2. Ion Sphere Particles containing libraries were deposited on theIon PI chip v2 or HiQ, respectively, and sequenced using the Ion Torrent Proton. Thisapproach generated an average of 23 million reads per sample (range 11  41 millionreads; Sup. Table 1). See Supplemental Experimental Procedures for details.