Difference between Normal tissue and Solid Tissue normal

[Piyal saha]

Dear Concern, 

When I am fetching data from the TCGA TARGET GTEX dataset to comapre between Tumor vs Normal tissue sample, one sample type is noted as 'Solid tissue normal'. Could you tell me what is the difference between Normal tissue and Solid tissue normal. I have seen a significant difference in gene expression between these two tissues.

Thank you. Kind regards,

Piyal

[Mary Goldman]

Hi Piyal, 

There are two sources of normal tissue in the TCGA TARGET GTEX dataset: matched normal from TCGA patients and normal tissue from GTEX. I recommend either adding the phenotypic data '_study' or looking at our raw data (https://xenabrowser.net/datapages/?host=https%3A%2F%2Ftoil.xenahubs.net&dataset=TcgaTargetGTEX_phenotype.txt) to see where these different normal tissues are originating. 

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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