normal sample of ovarian cancer in TCGA dataset

Question

[yueli7]

Hello,

I want to compare the fallopian tube (normal) and cancer samples form TCGA ovarian cancer patients.

Where can I find the fallopian tube (normal) sample? Is that "Solid Normal Tissue"?

Thanks in advance for great help!

yue

Answer 1

[Kevin Blighe]

Yes, Solid Normal Tissue is one of the 'normal' tissues that were used in the TCGA. You can infer whether a sample is from tumour or normal by its TCGA barcode. The fourth (4th) component of the TCGA barcode, a 2-digit number, indicates this:

• Tumour samples: 01 - 09
• Normal samples: 10 -19
• Control samples: 20 - 29

Further information:

• A: Meaning letters in TCGA sample barcode field
• github.com/kevinblighe/TCGAbarcode/TCGAbarcode.pdf
• Sample Type Codes

If you don't have the TCGA barcodes and just have file UUIDs or filenames, then you can [possibly] obtain the matching TCGA barcodes for these via these functions:

• UUID-to-TCGA Barcode: C: Sample names for TCGA data from GDC-legacy archive
• Filename-to-TCGA Barcode: C: problem in matching the names between file names and patients Id in TCGA

Best of luck, Kevin

[yueli7]

Hello, Kevin Blighe,

Thank you so much for your great help!

You told me so detailed knowledge!

Thank you again!

Yue LI

[Kevin Blighe]

谢谢 / Thank you!

Best of luck.

Kevin