How to get DNA and RNA datasets from GEO,TCGA and EBI
As a beginner, I would love to know what is the best steps to get data that contains specific requirements as I describe it below from major resource such as GEO, TCGA and EBI
- Whole Transcripitomic information - typically RNA SEQ or RNA Affymetrix MUST BE PRESENT
- Whole Exone or Whole Genome Sequencing (DNA) DNA Panel - test only for a subset of all the genes for mutations
- Patient Outcome (what drugs were given, how long did the patient survive) if possible
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Please edit your post and add a more descriptive title. Your current title is generic and gives readers no idea what your post is about. What's more, it takes away from the interest users might have in your post. See Rule #5 here: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202
@Milan your new title is no more descriptive than your old one. Please invest some more effort.
See this tutorial by Kevin Blighe - https://www.biostars.org/p/344233/
This is for affymetrix expression arrays.
Requirement #3 may be difficult to find in open datasets. You (or your PI) may need to create an account on dbGAP to access metadata.