Entering edit mode
9.6 years ago
ps1212
•
0
What are the questions that I should be asking when I do RNA-Seq trascriptome analysis of Alzheimers? I also have Exome data and Whole genome data from clinical samples. I am trying to find out the similarities, differences in expression of genes, eQTLs and variants/SNPs between HiPSCs (human induced pluripotent stem cells) and mature neurons that these HiPSCs have been differentiated into.
Do you have iPS/differentiated cells from both patients and controls? If not, there's nothing interesting to find. I've done something similar to this with Huntington's samples, so I'd be curious to find out about Alzheimer's samples.
I would explain a little bit the experiment design, otherwise is quite confusing to help with this. The question of Devon is quite important. As well, as number of samples, what exactly you have for each of them... I guess that mainly you want to see if there are germline mutation related to some RNA-expression. Or post-transcriptional evidence that are related to each group, or condition, or even somatic mutations.