Retrieval of RNA-Seq data related to TNBC from all databases.

Question

[fawazfebin]

Hi

I would like to retrieve the publicly available RNA-Seq data related to TNBC from all databases. What are the steps that I need to follow? Great thanks in advance.

Answer 1

[Kevin Blighe]

For TCGA triple-negative BRCA data, you can follow this: How to download triple negative breast cancer RNA-seq fpkm data from GDC.

For other data, look on these data repositories:

• European Nucleotide Archive
• European Genome-phenome Archive
• ArrayExpress
• Sequence Read Archive

There is also a lot of other cancer data available at the ICGC Data Portal. This is hosted by the ICGC and links to TCGA data at the GDC, and PCAWG (Pan-cancer Analysis of Whole Genomes) data at other global sites. For these, you will have to request access.

Kevin