Hello community, I am a bioinformatics novice so forgive my lack of knowledge; I need to download bulk RNA seq data for Acute Myeloid Leukemia and normal tissue (peripheral blood) to perform differential gene expression analysis in edgeR. I am having a hard time finding the datasets i need: someone suggested me to use firebrowse, others to look directly into TCGA. However, i am very confused by the amount of files and the whole process: could someone guide me? I don't need a huge amount of replicates as i just need a list of DEG to intersect with a list of candidates. The best would be to obtain the reads counts. Thank you very much.
edit: data from cell lines vs cd34+ cells would be okay too, if that's somehow easier to obtain
Is this an assignment of some sort? If you just need precomputed counts you could look at cBioPortal for the studies you are interested in. They also have tutorials available.
I'm taking a look right now, thank you very much! Anyway, yes it is a sort of assignment: it's a step of the workflow for my master thesis
edit: i really appreciate you help, but thats not exactly what i was looking for because there are no matched healthy controls