I would like to validate the results of RNAseq but I am not familiar with this. I currently have a table with Gene IDs (Ciclev10004574m.g for example) and their Arabidopsis homologs (AT5G52300.1 for example) and expression levels. I selected the DEGs based on p value and log2FoldChange. However, for the design of primers, I don't know if I should use the gene sequences from my species of interest or their homologs from arabidopsis? or are they the same thing?
You should use gene sequences from your species of interest in order to validate your RNA seq data by qPCR.
For my own project, I had Arabidopsis homologs as well as geneID from species of interest. And for validation of candidate genes using RT-qPCR, I used sequence information from the species of interest rather than Arabidopsis orthologue. I hope it helps.
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