Downloading Full mRNA expression (RNA Seq RPKM) for Cell Line Data Sets

[Nguyen, Vinh]

Hello,

 

I want to do some pathway analysis with a gene set of interest. I am analyzing the cell line data set ( Cancer Cell Line Encyclopedia, Cancer Cell Line Encyclopedia, NCI-60 Cell Lines ). I was able to use your platform to identify the samples that contained altered gene and unaltered genes. I also got the RNA for the altered genes as well. What I am missing is the mRNA data set for the unaltered samples. cBioportal said that it was too large a query and that I needed to reach out to you to get it.

 

Is there a way to get a file of mRNA for all the genes in CCLE and NCI-60?

 

If there are any questions you have feel free to ask

 

Best,

Vinh Nguyen

PhD Candidate

UNC-Chapel Hill

 

[Nikolaus Schultz]

Hi,

You can download the full expression data sets from our data hub at these links:

https://github.com/cBioPortal/datahub/tree/master/public/cellline_nci60

https://github.com/cBioPortal/datahub/tree/master/public/ccle_broad_2019

https://github.com/cBioPortal/datahub/tree/master/public/cellline_ccle_broad

Niki

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