title: RNA-Seq of Mus musculus: bone marrow
design: Total RNA was prepared from BMDM by RNeasy Mini Kit purification (Qiagen). The samples were subjected to Turbo DNase treatment (Life Technologies). Total RNA from each sample was quantified using a Qubit 3.0 Fluorometer. At least 1.5 g per sample was submitted to the CETI Molecular Biology Core at the University of New Mexico, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer. All samples had RIN values > 9.6, indicating the RNA was high quality. Libraries were prepared using the KAPA mRNA HyperPrep Kit with PolyA selection. Library quality was assessed using a Qubit and a Bioanalyzer. qRT-PCR of adapters was performed to determine the amount of library in each sample. Libraries were sequenced using an Illumina NextSeq 500 Sequencer generating paired-end, 75-bp read length sequences. 1 mid-throughput run (150 M theoretical maximum clusters) and 3 high-throughput runs (400 M theoretical maximum clusters) were performed.