Question: looking for TCGA gene expression Normal Samples
0
gravatar for Peter Chung
3.0 years ago by
Peter Chung80
Hong Kong
Peter Chung80 wrote:

I am looking for the matched cancer samples and normal samples in TCGA. I used to download these data before but now I seem like can't find the normal samples from the TCGA legacy archive.

I looked up the TCGA barcode and the samples all are cancer sample label 01 but didn't have 11 for the normal samples.

How can I download the normal samples from TCGA ?

Thank you very much for your help.

sequence genome • 2.1k views
ADD COMMENTlink modified 3.0 years ago by nwon40 • written 3.0 years ago by Peter Chung80
0
gravatar for nwon
3.0 years ago by
nwon40
New Zealand
nwon40 wrote:

I have just done this. Firstly, I believe you would need have been granted restricted access to the raw data at the very least.

Then, you will need to goto the GDC legacy archive. And with the facet search it is possible to add a biospecimen filter, search for sample id and enter 11 for normal tissue...........

ADD COMMENTlink written 3.0 years ago by nwon40

@nwon I tried to put 11 or 11a in the case id but it had shown not found anything and can you show me which field should i add in the biospecimen filter ?

ADD REPLYlink written 3.0 years ago by Peter Chung80

Hi Peter,

in facet search type in sample and it's sample type.....you can see to the left the facet term already activated, good luck!

Nick

GDC snapshot

ADD REPLYlink written 3.0 years ago by nwon40
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