Comparing expression of genes within an RNA-seq Experiment to confirm pluripotency

Question

[noahhelton98]

Hi All,

I have an RNA-seq dataset in which I have already analyzed differential gene expression across the control and experimental condition, however, I need to check the samples to confirm that the cells are still pluripotent (ie. expressing Sox2, Oct3/4 etc.) and not expressing neuronal progenitor genes. Is there a way specific way to this or any literature I should be looking at specifically? I understand how to do it for single cell RNA-seq, but my samples are total RNA from many cells. I am not sure if I should use another gene as a reference and compare the expression levels. I want to make a figure with this as well - so I need a way of measuring that can be done across all samples. If someone could point me in the right direction I would greatly appreciate it, Thank you!

Answer 1

[sysboolean]

Have you thought about plotting the normalized count values on a gene counts plot ? If you have a list of genes (pluripotent markers & neuronal progenitor markers), you could make this plot for your list and check expression for each gene across conditions.