Hello, I am currently doing a research on whether if there is any correlation between DNA methylation and their expression in non-small cell adenocarcinoma. I am using the TCGA study data from the GDC portal and I am wondering if I could find any normal and healthy sample tissues in that portal? if no is there a specific place where I could find that information? Thank you so much in advance!
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alihosseinzadeh023 •
2 answers
You can check out https://gtexportal.org/home/ also for the normal sample tissues you are looking for. But not sure if it will have data regarding methylation.
The phenodata tables associated to the data will tell you which samples are normal tissue or tumor. The XenaBrowser is quite useful to access (level 3) TCGA data. If you click in any cancer, it will show you if there is methylation, RNA-seq data available, and for how many samples, and you can download the data from there. You can download the phenotype table, and check which samples are tumorous or normal tissue (there is a column named "sample_type" or something like that which defines "Primary Tumor" or "Solid tissue normal" variables).
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