I would like to do an RNAseq comparison between the hippocampus and striatum during contextual fear conditioning. My main interest is to see differential expression for protein coding genes. However, as a side project, I think it would be interesting to see how expression changes for non-coding regions (for example, enhancer RNAs and some of the snRNAs involved in splicing).
I've analysed ribo-depleted data sets for human cell lines before and didn't have any issues but before going through with sequencing I wanted to make sure that no one else had run into any issues with ribo-depletion with different types of tissues. I haven't seen anything too worrying while searching through other threads but most of these aren't tissue specific. Has anyone else had any specific issues with ribo-depletion and sequencing in the brain (or I would also be interested to hear general sequencing issues with the brain)?
As a side question, why is poly-A sequencing still so commonly used? It's been shown that non-coding RNAs are prevalent and play a major role in all cell types and I don't understand why people wouldn't just make ribo-depleted libraries so that they could consider those effects on non-coding RNAs. Why isn't ribo-depletion the norm?
Thanks so much for any suggestions and discussion!
I've analysed ribo-depleted data sets for human cell lines before and didn't have any issues but before going through with sequencing I wanted to make sure that no one else had run into any issues with ribo-depletion with different types of tissues. I haven't seen anything too worrying while searching through other threads but most of these aren't tissue specific. Has anyone else had any specific issues with ribo-depletion and sequencing in the brain (or I would also be interested to hear general sequencing issues with the brain)?
As a side question, why is poly-A sequencing still so commonly used? It's been shown that non-coding RNAs are prevalent and play a major role in all cell types and I don't understand why people wouldn't just make ribo-depleted libraries so that they could consider those effects on non-coding RNAs. Why isn't ribo-depletion the norm?
Thanks so much for any suggestions and discussion!
Comment