Probing the unfolded protein response to mouse hepatitis coronavirus infection through RNA sequencing and ribosome profiling

Georgia M. Cook; Katherine Brown; Krzysztof Franaszek; Nathan A. Moore; Stuart G. Siddell; Ian Brierley; Andrew E. Firth; Nerea Irigoyen

Shrinkage of the transcriptional fold changes to reduce noise in lowly-expressed genes was applied 501 using lfcShrink (parameter: type='normal'). 502 503 A given gene was considered to be differentially expressed if the FDR was less than 0.05 and the 504 fold change between the averages of infected and mock replicates was greater than two. Volcano 505 plots and transcription vs TE comparison plots were generated using standard R plotting features The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/292979 doi: bioRxiv preprint 4 EDTA, 0.5% NP40). Cell lysate aliquots were mixed with Laemmli's sample buffer to a final 577 concentration of 1× and subjected to 10% SDS-PAGE followed by autoradiography. 578 579 TCID 50 assays: Virus replication was assessed using a 50% tissue culture infective dose (TCID 50 ) 580 assay. One day prior to infection, 17 Cl-1 cells were seeded in 96-well plates at 4 × 10 3 cells/well in 581 a final volume of 100 µl/well. Supernatant derived from extracellular media (released virions) or 582 from extracellular media and cells subjected to a cycle of freezing/thawing (intra-and extracelluar The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/292979 doi: bioRxiv preprint 1 The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/292979 doi: bioRxiv preprint