I think new forms of digital expression are interesting and laudable — I'm a big fan of Snapchat's experimentation with the medium and wish others would take risks like it has.
The gene- and exon-level digital expression is inferred by the approach presented in the Methods section.
Read mapping, read normalization and global digital expression were carried out by the bioinformatics department of Sick-Kids Hospital, Next Generation Sequencing service (Vancouver, Canada).
In order to understand the impact of JA and MeJA on L. gmelinii at the transcriptional-level, the analysis of differentially expressed genes (DEGs) using digital gene expression was conducted.
Digital gene expression was assessed using DESeq.
Differential digital gene expression was deemed with FDR value ≤0.001 and |log2 Ratio| ≥ 1 in sequence counts across libraries.
Digital gene Expression was carried out by DEGseq package in R-bioconductor 2.15 for each library with reference to control.
Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries.
To further determine the tissue-specific gene expression of select genes, digital gene expression was carried out for DREB and NAC TFs, OMT gene, and miRNA 172 targeting site genes in wheat transcripts (Supplementary Fig. S2).
For each ORF a digital measurement of expression was obtained by counting the total number of reads that align to it (Fig. 1A).
