Question: download tumor and normal data from TCGA
1
gravatar for Ben
14 months ago by
Ben50
Ben50 wrote:

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 • 1.1k views
ADD COMMENTlink modified 14 months ago • written 14 months ago by Ben50

thanks a lot! thanks again

ADD REPLYlink written 14 months ago by Ben50
1

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

ADD REPLYlink written 14 months ago by genomax52k
1
gravatar for andreslanzos
14 months ago by
andreslanzos50
andreslanzos50 wrote:

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 COMMENTlink written 14 months ago by andreslanzos50

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 REPLYlink written 14 months ago by genomax52k

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

ADD REPLYlink written 13 months ago by Ben50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 661 users visited in the last hour