RNA-Seq of mus musculus: trVLP-infected RAW264.7
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturers instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligo (dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand complementary DNA (cDNA) were subsequently synthesized, incorporating UMIs during reverse transcription. cDNA fragments were end repaired and adenylated at 3 ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).