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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.
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.
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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.
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.
Inspecting the expression profiles of Ctnnb1 and its associated proteasome related genes shows a different expression in the LF compared to the HF group at t = 48, so this mechanism could be affected by diet in the late response to the glucose challenge.
Additionally, we inspected the gene expression of CYP6E14 and CYP6AE11 (with 91% nucleotide identity to CYP6E14) across all gossypol concentrations by qRT-PCR (See additional file 17 Figure S3) CYP6and4 and CYP6AE11 are highly up-regulated at the highest gossypol concentration.
For that, we inspected the genes whose expression was changed consistently in the three individual stages as these may be linked with a putative genetic variation (possibly in their regulatory elements).
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