How to get Normal Samples from TCGA?

Question

[Jaber]

Greetings BioStars,

I recently came across a study that utilized the TCGA-LIHC dataset in their pipeline, including data from 50 normal liver patients. I’m curious about how they obtained such a large number of normal samples, as I couldn’t find them through GDC or TCGA-Biolinks.

Aside from GEO, are there other reliable sources where normal samples for bulk RNA-seq can be accessed?

I appreciate your help!

[GenoMax]

Normal samples may still require approval for access due to privacy concerns, especially if you are looking to get the original sequence data.

[Jaber]

Thank you, I just want the transcriptomic data, no need for the raw data

[GenoMax]

came across a study that utilized the TCGA-LIHC dataset in their pipeline, including data from 50 normal liver patients.

Do you know if they used "normal" data from TCGA or was it from some other source.

[Jaber]

they didn't explicitly mention, but it appears from the same dataset,

Here is the link for the study https://pmc.ncbi.nlm.nih.gov/articles/PMC11621542/

[aUser]

You can use TCGA-Biolinks to download the normal samples (final files, not the raw data) from TCGA, I do not know why it is not working for you.

GTeX is another resource to download normal data. It has only the normal samples.

https://gtexportal.org/home/

[Jaber]

Thank you so much,

I use this code to access the TCGA-LIHC

clin_liver <- GDCquery_clinic(project = "TCGA-LIHC", type = "clinical")
View(clin_liver)

no normal case I could identify,

I'll try gtexportal