Fig. 1

Proteomics Informed by Transcriptomics workflow. (i) Cells are adapted to SILAC media containing Lysine and Arginine with isotopes of Carbon and Nitrogen. Cells were infected with NBV for 0 (control), 8 and 24 h using an MOI of 1.5. (ii) Total RNA was isolated and mRNA sequenced, using 100 base pair paired-end reads. (iii) Reads obtained from sequencing, were quality trimmed and transcripts assembled de novo using Trinity. Assembled transcripts were annotated using BLASTx against the non-redundant UniProtKB/SwissProt protein database. (iv) Sequence reads are mapped back to the de novo assembled transcriptome using Bowtie2. (v) Differential gene expression testing was calculated with expression values relative to 0 h control determined by DESeq. (vi) The de novo transcriptome was translated in 6 frames as a database for MS. (vii) Extracted proteins were separated by SDS-PAGE and digested via in-gel trypsin digestion. (viii) Peptides were analysed by LC-MS/MS and the (ix) MS spectra searched against the 6-frame translated de novo transcriptome. (x) Peptides are compiled into proteinGroups and the differential expression is calculated using MaxQuant