download tumor and normal data from TCGA

Question

[Ben]

I plan to download tumor and normal RNA-seq data from TCGA database. However, I only download tumor RNA-seq data, could anyone help me to download normal RNA-seq data from TCGA database?

[Ben]

thanks a lot! thanks again

[GenoMax]

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Answer 1

[andreslanzos]

Hi,

Not for all tumour samples there is a matched normal sample. But your can check how many normal samples there are:

1) Go to the data portal of TCGA: https://portal.gdc.cancer.gov/search/s?facetTab=cases

2) Click on "Add a Case/Biospecimen Filter" at the left part.

3) Search for this field: "samples.sample_type" with description: "Text term to describe the source of a biospecimen used for a laboratory test."

4) Now you will see how many files there are for normal, tumour, etc:

Primary Tumor 9,983

Blood Derived Normal 8,876

Solid Tissue Normal 2,333

Metastatic 398

Primary Blood Derived Cancer - Peripheral Blood 189

Bone Marrow Normal 179

Primary Blood Derived Cancer - Bone Marrow 164

Recurrent Blood Derived Cancer - Peripheral Blood 91

Recurrent Tumor 60

Fibroblasts from Bone Marrow Normal 28

Blood Derived Cancer - Bone Marrow, Post-treatment 21

Additional - New Primary 11

FFPE Scrolls 5

Buccal Cell Normal 5

Additional Metastatic 2

Blood Derived Cancer - Peripheral Blood, Post-treatment 1

[GenoMax]

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[Ben]

Thanks a lot! But I can not determine which tumor and normal samples are matched, do you know how to select matched samples?

Answer 2

[H.Hasani]

The sample ID contains that information: the first 4 letters indicate project name, e.g. TCGA

second two digits: tissue source

third 4 digits: patient ID

fifth 3 combinations: two digits representing sample type (1-9 tumor, 10-14 normal)

my note on the previous answer is that the data I downloaded didn't match the numbers they provide on the webside!