qRT-PCR for Xbp1 (unspliced) and Xbp1s (spliced) was performed with Custom TaqMan gene expression assay primers and probes (Applied Biosystems) using the sequences published previously.
Whenever possible, the full coding sequence of the catalytic domain and of the adjacent regions was assembled using the sequences of published cDNAs and overlapping ESTs.
The outcomes of the BLAST searches using the representative sequences published for the 12 TEs as the queries revealed the total hit numbers, alignments of the hit sequences, and the bit scores.
For the TRBV/TRBC gene assay design, we used the gene sequences published at the Immunogenetics Database [http://imgt.cines.fr/] according to ABI recommendations using the Primer Express Software (version 2.0; ABI).
To prove the applicability of our plant transient system for the production of anticancer mAb, we synthesized genes encoding the heavy and light chains of the trastuzumab protein using the amino acid sequence published in DrugBank (accession number DB00072) and constructed 35S-based vectors (35S-LC and 35S-HC) (Figure 1A).
Using the published sequences from HPRS-103 (ALV-J isolated in 1989 in Great Britain), we designed a set of PCR primers that amplified proviral DNA from nine U.S. field samples.
Assays for IL-1β, tumor necrosis factor-alpha (TNF-α), and interferon-beta (IFN-β) were designed using the published sequences for these genes and Primer Express software (Applied Biosystems, Warrington, United Kingdom) and quantified using a relative standard curve.
Assays for IFN-α, IFN-β, IL-10, IP-10, IRF-7, TLR3, RIG-I, PKR, OAS, Mx1, Bax, Fas, IFNγ, and all T cell transcripts were designed using the published sequences for these genes, applied to Primes Express™ software.
Because of the sequencing protocol used, the published sequence of strain SS14 [27] contained the same sequence error in position 157003 157004.
