Processed Data
CCLE data
Broad DepMap Portal : The most recently processed and up-to-date CCLE datasets along with many perturbation datasets.
List of Cell lines
Genetic Data
Merged mutation calls (Coding regions, germlin filtered)
CCLE structural variants (SvABA calls) for 329 cell lines
CCLE ABSOLUTE copy number analysis results
Copy-number values per gene
Segmented copy-number profiles in the .seg file format. (hg19)
RNA Expression Data
CCLE RNAseq gene expression data for1019 cell lines (RPKM)
CCLE RNAseq gene expression data for1019 cell lines (RSEM, gene)
CCLE RNAseq gene expression data for1019 cell lines (RSEM, transcript)
CCLE RNAseq gene expression data for1019 cell lines (read counts)
CCLE RNAseq gene expression data for1019 cell lines (Exon inclusion ratios)
CCLE RNAseq gene expression data for1019 cell lines (Exon inclusion ratio denominator)
Gene definitions (GENCODE19, GTEx7)
CCLE miRNA expression data
Fusion calls
Fusion calls for 1019 cell lines (filtered)
Unfiltered STAR-Fusion calls
Epigenetic and Histone Modification Data
DNA methylation by RRBS
Promotor Methylation - 1 Kb upstream of the promotor
Promotor Methylation - CpG clusters
CCLE DNA methylation data (CpG islands)
Enhancer Methylation (557 enhancer regions from VISTA
RRBS - raw sequencing reads
RRBS - processed data ? (a-d above)
Bulk Histone H3 modifications by Mass Reaction Monitoring (MRM)
CCLE Global Chromatin Profiling data
Proteomics Data
CCLE Reverse Phase Protein Array (RPPA) data
RPPA antibody information
Mass spectrometry data
Metabolomics Data
CCLE metabolomics dataset (clean, imputed)