Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Paired-end ribosome profiling of MARC-145 cells infected with porcine reproductive and respiratory syndrome virus (PRRSV)-2, harvested at 9 hpi


ABSTRACT: MARC-145 cells were infected with porcine reproductive and respiratory syndrome virus (PRRSV)-2 isolate SD95-21 (KC469618.1), and a mutant thereof (KO2), and subjected to ribosome profiling to analyse the viral and host translatome, frameshifting on the viral genome, and putative frameshift-related ribosome pausing events. Samples were harvested at 9 hpi by flash-freezing, without cycloheximide pre-treatment. RNase I treatment was carried out, following which ribosomes and enclosed RNA were isolated by centrifugation through a sucrose cushion. RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 19-80nt long. Fragments were cloned into adapters based on the TruSeq small RNA adapters, with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a paired-end run. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Chlorocebus sabaeus

SUBMITTER: Georgia Cook 

PROVIDER: E-MTAB-10622 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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