The issues on CCLE dataset

[Zhicheng Zhou]

To whom it may concern:

I hope this message finds you well.

I am writing to bring to your attention an issue I encountered with the CCLE dataset. Specifically, I am attempting to subgroup the CCLE skin cell lines and conduct Gene Set Enrichment Analysis (GSEA) based on the expression of the ADAR gene. However, I have encountered an error message indicating that the gene expression file cannot be found at the following URL

'https://ucscpublic.xenahubs.net/download/ccle/CCLE_DepMap_18Q2_RNAseq_RPKM_20180502"

II would greatly appreciate your assistance in resolving this issue so that I can proceed with my analysis.

Thank you for your attention to this matter. I look forward to your response.

Best regards,

Zhicheng Zhou

[Mary Goldman]

Hi Zhicheng Zhou,

Apologies, CCLE has requested that we only visualize their data. If you would like to run a GSEA on the data from CCLE, you will need to download their data yourself and run it through Appyter (https://appyters.maayanlab.cloud/#/Bulk_RNA_seq) or a similar tool.

Link to CCLE: https://sites.broadinstitute.org/ccle/

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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