Question: GDAC firehose, multiple samples from RNASeq corresponds to the same clinical data
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gravatar for xuren2120
4 months ago by
xuren212010
xuren212010 wrote:

Hi everyone,

I have a question about the GDAC firehose data from this website: (https://gdac.broadinstitute.org). I downloaded the RNASeq data: illuminahiseq_rnaseqv2-RSEM_genes and clinical data: Clinical_Pick_Tier1, and I found multiple columns in RNASeq corresponds to the same column clinical data. e.g. In BRCA:

In RNASeq data, there are columns:
TCGA-BH-A208-11A-51R-A157-07 TCGA-BH-A208-01A-11R-A157-07

However, in the clinical data, there is only one column:
TCGA-BH-A208

I have two questions:
1) Is the sample TCGA-BH-A208 a tumor sample or normal sample?
2) If I wish to match the clinical data to RNASeq data, since there is only one clinical column but two RNASeq columns, which RNASeq column should I use?

I'd appreciate it if anyone could help. Thanks.

rna-seq sequence tcga • 223 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe45k • written 4 months ago by xuren212010
1
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe45k
Kevin Blighe45k wrote:

One cannot infer anything about the tissue type from the short TCGA barcode, i.e., TCGA-BH-A208. We can just say that this is an individual who was part of the TCGA project. It then follows that:

  • TCGA-BH-A208-11A-51R-A157-07 = normal tissue from patient with barcode TCGA-BH-A208
  • TCGA-BH-A208-01A-11R-A157-07 = tumour tissue from patient with barcode TCGA-BH-A208

Take a look at the definitions of the fields in these barcodes: Meaning letters in TCGA sample barcode field

Kevin

ADD COMMENTlink written 4 months ago by Kevin Blighe45k
1

Got it, thanks Kevin!

ADD REPLYlink written 4 months ago by xuren212010
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