Blood Derived Normal RNA_seq samples TCGA
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16 months ago

Hi, does anyone know if there are any Blood Derived Normal samples with RNAseq data in any of the TCGA databases? I want to compare exon quantification between normal and cancer samples but I can't find any normal blood samples.

Thanks

RNA-Seq TCGA • 928 views
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Hi I'm facing the same problem now .i want to ask whether this problem has been solved or not ? If it had been solved, could you please tell me the way to solve it?

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16 months ago
dsull ★ 2.3k

There are blood derived normal samples for many solid tumors (e.g. breast cancer). Edit: Not for RNA-seq though.

If you want blood derived normal samples for blood cancers such as lymphoma/leukemia, you won't be able to find any.

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16 months ago
khorms ▴ 210

I don't think there are any. In order to double check, you could do this:
This table show the codes for sample types; so all you need to know to figure out what kind of sample you are looking at is the last two digit barcode.
You could go to Xena, look at the pages corresponding to the cancer types of your interest and check if there are any samples with the corresponding barcode.
I didn't find any but what if I'm missing something

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16 months ago
newbio17 ▴ 340

As @khorms mentioned, there doesn't seem to be any RNA-Seq data for TCGA blood-derived normal samples available on TCGA. You can quickly check this by using the filters to explore the repository page on GDC. I've also checked legacy repository, but still couldn't find anything. You can email GDC support for a confident answer if you'd like to double check.

Also, is there a reason as to why you want to use blood-derived normal samples (not familiar with exon quantification pipelines) instead of solid tissue normal samples? There's probably differences in expression levels between a normal tissue and a blood sample. To my understanding, this is why researchers utilize matched normal tissue samples to examine normal vs. cancer for their study.

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Thank you. The reason is because I want to examine differences between blood samples for leukemia and normal blood samples.

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