Leukemia vs peripheral blood (bulk) RNA seq data retrieval
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4.0 years ago
Oli • 0

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

RNA-Seq • 818 views
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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.

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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

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