title: GSM9478846: BMDM KO, uninfected,  24H, biol rep 3; Mus musculus; RNA-Seq
library_construction_protocol: After 4 or 24 h of infection, samples were lysed using TRIzol (Invitrogen, 15596018) for 5 min, incubated with chloroform, and centrifuged at 12,000 x g for 5 min at 4 °C. Then, the aqueous phase was subject to RNA extraction using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer's protocol. Samples were analyzed on an Agilent Tapestation 4200 to determine level of degradation to ensure that only high quality RNA was used (RIN Score 8 or higher). We used a Qubit® 4.0 Fluorimeter (ThermoFisher) to determine RNA concentration prior to starting library prep. One microgram of total DNAse treated RNA was then prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Poly-A RNA was purified and fragmented before strand-specific cDNA synthesis. cDNA was then A-tailed and indexed adapters ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200. Before being normalized and pooled, samples were quantified by Qubit then sequenced on the Illumina NextSeq 2000 using a P2-100 flowcell.