To examine which of the miRNA family members are more abundantly expressed in rice seedlings, we inspected the expression profile of known miRNAs in untreated seedlings (control library) based on their sequence frequencies.
First, we inspected the expression profiles of the Vitis vinifera stilbene synthase gene family [ 19] throughout our experimental design.
We then inspected the expression levels of the A-IPACs and their respective targets to provide possible mechanisms of gene expression regulation.
We inspected the expression patterns of SMB on GENESTIGATOR [ 67] but failed in an attempt to find any clues for their diversified roles in secondary wall formation.
After choosing samples in the "Sample Tree", the user could visually inspect the expression profile through a bar chart, and add mean expression for similar samples (i.e. samples in the same group) if needed.
To examine this possibility, reverse transcriptase PCR (RT-PCR) was used to inspect the expression of all members of the DCL, AGO, RDR and Double-stranded RNA binding protein (DRB) genes.
Accordingly, we first inspected the expression of genes from the upstream isoprenoid precursor biosynthetic pathways, namely the cytosolic MVA pathway and the plastidial MEP pathway, in our RNA-seq data.
In order to inspect the expression pattern of tRFs in abiotic stress treatments, we conducted an analysis of the AlaAGC, ArgCCT, ArgTCG and GlyTCC 5' tRFs, using the available deep sequencing data.
When inspecting the cluster of expression of mtDNA-encoded subunits, ND4L presented a significantly distinct pattern, which diverged from those of the other mtDNA-encoded subunits.
We independently validated the normalization in every dataset by inspecting the distribution of expression values.
