How can I get control RNAseq data?

Question

[Kateryna]

Hi everyone,

I just start to learn bioinformatics and I want to try myself in analyzing some TCGA data. For example, I am interested in kidney cancer and I wondered where can I find any control (normal) samples?

In addition to it, it will be extremely helpful if anybody will suggest some resources for effective learning how to work wit data analyzing (except well-known coursera, edx and other).

Thank you for any future suggestions!

Answer 1

[raunakms]

For some of the cancer types in TCGA, RNAseq profile of Normal samples are also present. You can look at the TCGA-barcode IDs of the individual samples and identify if its a Tumor or Normal (See here: https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode).

Alternatively, GTEx project has a large collection of RNAseq profiles of different tissues (non-cancerous) (http://www.gtexportal.org/home/)

[Kateryna]

Thank you, but how can I download kidney tissues RNA-seq files from GTEx?

[raunakms]

Look at the download section in the GTEx website (http://www.gtexportal.org/home/), look at the sample ID that matches to kidney tissues and download it !!!