Details about samples from TCGA KIRC data

[Hemasri Sai]

Dear Concern, 
I fetched my data from Xena browser data sets:miRNA mature strand expressions  RNA-seq -illuminaHiseq. Link

There are a total of 311 samples. 

1. Do all 311 samples have kidney clear cell carcinoma? 
2. Are  311 samples from 311 different individuals? 
   
3. Is solid tissue normal means those samples don't have cancer. i.e. completely healthy.
   
4. In the sample name example TCGA-CZ-4863-01. what exactly 4863 represents?
   
5. If I see samples like TCGA-CZ-4863-01 and TCGA-CZ-4863-11 where only the sample type is different. is it from the same individual?

Thankyou in advance.
Regards,
Hema

[Mary Goldman]

Hi Hema,

These 311 samples contain both tumor and solid tissue normal from a number of individuals. Please see this file and look at the column 'sample type' to see which sample is which: https://xenabrowser.net/datapages/?dataset=TCGA.KIRC.sampleMap%2FKIRC_clinicalMatrix&host=https%3A%2F%2Ftcga.xenahubs.net.

The solid tissue normal is tissue that was adjacent to tumor tissue and was deemed to be normal by the pathologist. Some patients donated both tumor tissue and solid tissue normal to this study.

I believe this page will be helpful in understanding the TCGA barcodes: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/ If you have any questions, please let us know.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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