How to use TCGA miRNA seq data?

Question

[bhoomisharma04]

I have downloaded miRNA seq data for colon adenocarcinoma. As i am a beginner, i am facing difficulties to understand and interpret the data. I have miRNA seq files for all samples but how to find the file for the matched normal tissue? And how to study the expression of a particular miRNA across the whole sample set?

Answer 1

[Na Sed]

When you download data from TCGA, it includes a text file, named "FILE_SAMPLE_MAP". In this file you can find the patient codes as well as corresponding file names.

If you seek matched normal/tumor samples, you must note to the barcode of patients. The 'participant' part of barcodes must be the same. For more information about TCGA barcodes, please see this.

[acc.inpro321]

Sir, how to know whether a particular sample is healthy or cancerous? I just see expression data and no label. Where can I find it?

[Na Sed]

Please see the page that I have referred. In this page, as written, two digits in barcodes are "Sample". In the next table, it has been written that "Tumor types range from 01 - 09, normal types from 10 - 19 and control samples from 20 - 29."