RNA-seq dataset of experiment and control group of TARGET-ALL project in TCGA portal

Question

[song83244829]

Hi everyone,

I'm new to TCGA.

I want to use the open-access RNA-seq data of Acute lymphoblastic leukemia in the TCGA portal and found TARGET-ALL projects.

But I was confused by the repository.

1. The RNA-seq file name ID doesn't match with the sample ID, Case ID, or any ID in the profile.
2. In the Biospecimen file, they point out control and experimental sample ID, however, in RNA-seq count files, there is no corresponding files.

For example,

In Case ID: TARGET-10-PASFHR project ID: TARGET-ALL-P2 Case UUID: a982e88f-8527-5e48-a1d3-0b3bf9460c21

However, if you go to their RNA-seq file category, you would only find the files starting with:

ae8e64df-1f7b-443d-8103-11c8bb8b2a4b.rna_seq.augmented_star_gene_counts.tsv

and I can't tell if this is an experiment or a control.

any input is appreciated.

Thanks!!!!

Answer 1

[Kevin Blighe]

Hi,

Please take the HTSeq data from the Xena Browser, where there is also accompanying phenotype / metadata:

• https://xenabrowser.net/datapages/

I am currently working on this data and IDs match between expression and metadata.

Kind regards,

Kevin

[song83244829]

Thank you!!