Total RNA-Seq in HSV-1 infected mouse trigeminal ganglia explants
Female 8-week-old BALB/cAnNTac mice were infected with 10^5 PFU HSV-1 (strain 17) via the ocular route. Latently infected trigeminal ganglia were harvested five weeks after primary infection. Ganglia were explanted into culture for 12 hours in the presence of Vehicle (DMSO) or 2 M JQ1+ (Cayman Chemical CAS: 1268524-70-4). If indicated, 100 uM acyclovir (ACV) was added to explant culture media. Pooled ganglia were homogenized in 1 ml TriPure Isolation Reagent (Roche) using lysing matrix D on a FastPrep24 instrument (3 cycles of 40 seconds at 6 m/s). 0.2 ml chloroform was added for phase separation using Phase Lock Gel Heavy tubes and RNA isolation from the aqueous phase was obtained by using ISOLATE II RNA Mini Kit (Bioline). ERCC spike-ins were added to total RNA. rRNA depletion was performed and samples sequenced on Illumina NovaSeq6000 to generate 150 PE reads.