Good day all,
So I have been trying to retrieve RNA-seq, miRNA-seq and protein expression data from TCGA' GDC data portal. Unfortunately, I have been having some issues. I have read a number of previous posts here in biostars and other forums, but still having issues using the new GDC portal
I have figured out how to get the Primary Tumor and Solid normal tissue RNA-seq and miRNA-seq datasets I need i.e. TCGA barcode ids with 01 or 11 code respectively - as defined by https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes
For example TCGA-COAD project has 456 RNA-seq files and 444 miRNA-seq files
However, I am unable to find the corresponding protein expression datasets - especially Solid normal tissue datasets(11 code or any other). I have looked at TCPA - https://tcpaportal.org/tcpa/ and only found Primary tumor protein expression (01 code) for the TCGA projects I need. I have also looked through the legacy GDC portal but was unable to find any way to match the files names to the TCGA barcodes. In the new GDC portal I can put files in my cart and download the "sample sheet" which gives me the mapping of actual filenames, MD5 hashcodes, TCGA barcodes, etc. I honestly was under the impression that GDC would have the protein expression data as listed in this link - https://cancergenome.nih.gov/abouttcga/aboutdata/datalevelstypes
Am I missing something here? are my assumptions wrong on that Solid normal tissue datasets(11 code) are included? Amy help would be greatly appreciated.
