We designed 95 pairs of primers for base-substitution verification (supplementary table S2, Supplementary Material online) and 96 pairs of primers for indel verification (supplementary table S3, Supplementary Material online) with BatchPrimer 3 (You et al. 2008).
The code and data to reproduce all results from this analysis are provided in the supplementary material for verification and reuse (see Additional files 1, 2, and 3).
Supplementary Table 2 Verification cohort clinical characteristics.
Fragments were extended using RACE PCR (SMART RACE cDNA kit, Clontech), and used as templates for DIG-labeled in situ probes and dsRNA fragments following sequence verification (supplementary material Table S1).
Searched on the pathway bridge that has been enriched through prostate cancer pathways, the top 10 out of 88 forecasted paths were picked for further biological meaning verification (Supplementary Table 1.2).
Empirically, we can put forward two supplementary propositions: P3 for verification and P4 for falsification of SE definitional components.
Splicing analysis identified ∼350 genes with significant (P < 0.001) changes in splice site representation (Supplementary Table S3, independent verification in Supplementary Fig S3); however, the majority of transcripts altered in splicing were not altered in abundance compared to wild-type.
The sources of these, their culture conditions and DNA fingerprint data used for identity verification are summarised in Supplementary Table 2.
The double or triple mutants; wrky33 nced3, wrky33 nced5, wrky33 nced3 nced5, gh3.2 gh3.3-1, and wrky33 gh3.2 gh3.3 were generated by crossing single or double mutants followed by PCR-based verification using appropriate primers (Supplementary file 6).
The sequences of primers used for plasmid construction, gene replacement, verification, and sequencing are described in supplementary figure S1.
