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TCGA samples

Dears, I am working on the TCGA-LAML project and make a differential expression analysis between cases and control, but while open the sample sheet, I didn't find control samples, please find the attached photo for samples of sample ID and sample type in the sample sheet

enter image description here

So anyone can help how can I get the control samples for this project ?

tcga samplestype
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written by mrashad mrashad

1 answer

These samples are bone marrow aspirates. There are, indeed, neither matched healthy control samples nor matched normal tissue samples from the blood or marrow of each patient for this cohort; however, within the cohort are 'normal' cytogenetic abnormality sub-types. In this way, the within-cohort comparison could be conducted across sub-types (comparisons against 'normal'). More information on this is in the clinical data: https://portal.gdc.cancer.gov/files/c07a64a0-7588-4653-95ef-982b41a1a804

Otherwise, if you want a true healthy control, you may have to search public studies and download the raw data.

Kevin

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written by Kevin Blighe Kevin Blighe

Thanks for this fruitful answer, it helps me a lot

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written by mrashad mrashad

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