dSLAM-seq of MCMV

Swiss murine embryonic fibroblasts (NIH-3T3) were infected with wild-type Smith strain mouse cytomegalovirus (MCMV) at a multiplicity of infection (MOI) of 10. Metabolic RNA labelling was performed using 400µM 4sU for one hour prior to cell lysis. Total RNA was isolated using the Trizol protocol and U-to-C conversions were induced by IAA treatment according to the SLAM-seq protocol (Herzog et al., Nature Methods 2017). Sequencing libraries were prepared using the dRNA-seq protocol from the indicated time points of infection as described by Whisnant A.W. et al, Nat. Commun (2020). Overall design: MCMV infection was conducted on NIH-3T3 cells at an MOI of 10. Nascent RNA was labelled with 400µM 4sU one hour prior to RNA harvesting. 4sU labelled RNA was subject to alkylation to mediate U to C conversions to track newly synthesized RNA through GRAND-SLAM. Sequencing was conducted for total purified RNA obtained . Two biological replicates were performed for each of the time points: 0,1,2,4,6,12,18,24, 36, 48, 72 hpi. One biological replicate utilised phosphonoacetic acid and cycloheximide pre-treatment Please note that MCMV_tss.tar.gz contains a list of transcription start sites which are determined based on both dSLAM-seq and cRNA-seq datasets.