Sure, the main effect would be on the expression profile of genes. The ease or difficulty of RNA extraction would be not a major issue and would not be very significant in the results.

I would expect the transcriptome, say, in a growth cone to be quite different from, say, senescent tissue like autumn leaves.

In addition, older tissue would have cell walls that are harder to break, and, as you said yourself, more interfering substances. So the extraction yield would likely be lower.

Hi Mabrur, it is a very well-known fact that transcriptome expression is highly variable and is age-specific, time-specific, gender-specific, organ / tissue specific, environment-specific and also differs individual to individual and the same matters for plants too. It all depends what you are trying to find in the transcriptome and does that entity have any impact on its expression profile due to any or all of the above-mentioned factors and based on this decide whether it is better to go for transcriptome mapping or transcriptome assembly in your case. Also you need to take in account several other factors like adopting proper extraction protocols, yielding good proportion of the transcriptome you are interested (coding / non-coding / whole), good library preps, and using proper transcriptomic controls for judging assay variations, use substantial amount of replicates (biological and technical both) etc. Only then you can rely on the results of the transcriptome experiments.

Regards...