TCGA RNAseq normal and tumor samples problem
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8.0 years ago
morovatunc ▴ 550

Hi,

First of all, I want to clarify that I dont think TCGA can do RNA seq only for tumor sample? This is nonsense. This information must be somewhere. So, Can I reach this information with TCGA-Assembler.

  1. referring to this post

TCGA: Does TCGA cancer studies have mRNA expression data for Control/Normal samples? I tried to use TCGA-Assembler however it does not give this information neither. Is TCGA-assembler let you download data that cannot be seen by the Data matrix? or It just eases the download procedure ? Because that I understood from the answers was not all the information was visible in data matrix so this R package allows to download all of them ?!?

  1. When I checked the entries one by one, even though some of the entries have tumor and normal pairs, big majority of them are either only tumor or normal. I think this is wrong?

Any information is useful.

Thank you for your help,

Best,

Tunc.

RNA-Seq TCGA • 2.9k views
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Entering edit mode
8.0 years ago
Amitm ★ 2.2k

hi, AFAIK, not all TCGA cohorts have tumor-normal paired samples for RNA-seq. Some studies have e.g breast-cancer, and some dont like SKCM. If you look at this recent study, they analyzed all cohorts in TCGA RNA-seq which had paired normal available. You can restrict yourself to these cohorts (mentioned in the article) only if you want paired controls.

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8.0 years ago

For most cancer types, you will typically find tumors without paired normals (but you should almost never find normals without tumors).

Try comparing those resources to the TCGA FTP data:

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/

For example, for breast cancer see nationwidechildrens.org_biospecimen_sample_brca.txt in https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/brca/bcr/biotab/clin to map patients to samples

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