download tumor and normal data from TCGA
2
1
Entering edit mode
5.2 years ago
Ben ▴ 50

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?

next-gen • 6.1k views
ADD COMMENT
0
Entering edit mode

thanks a lot! thanks again

ADD REPLY
1
Entering edit mode

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLY
2
Entering edit mode
5.2 years ago
andreslanzos ▴ 60

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

ADD COMMENT
0
Entering edit mode

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
3.7 years ago
H.Hasani ▴ 990

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!

ADD COMMENT

Login before adding your answer.

Traffic: 1353 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6