Translational Genomics Research Institute: Quantified Cancer Cell Line Encyclopedia (CCLE) RNA-seq Data

Many applications analyze quantified transcript-level abundances to make inferences.  Having completed this computation across the large sample set, the CTD2 Center at the Translational Genomics Research Institute presents the quantified data in a straightforward, consolidated form for these types of analyses.

Experimental Approaches

After downloading RNA-seq data for 935 cell lines from the Cancer Cell Line Encyclopedia (CCLE), transcript-level abundance was quantified using Salmon1. All data were aligned using Salmon 0.4.2 using Homo Sapiens GRCh37.74 for reference. The resulting 935 quantification files, named by sample ID, have 4 columns for ensemble gene ID, length, number of reads, and transcripts per million (TPM). Other Salmon arguments were "--libType IU" (inward, unstranded).

If you have additional questions, please contact Gil Speyer


Access the CTD2 Data Portal.


  1. Patro R, et al. (2015). Accurate, fast, and model-aware transcript expression quantification with Salmon.
Last updated: May 11, 2017