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Cancer Cell Line Encyclopedia (56.2GB)

     Include previously released (deprecated) files

DNA Copy Number  (41.6GB) Affy SNP  (Published) 

Affymetrix SNP6.0 arrays.
Raw Affymetrix CEL files were converted to a single value for each probe set representing a SNP allele or a copy number probe. Copy numbers were then inferred based upon estimating probe set specific linear calibration curves, followed by normalization by the most similar HapMap normal samples. Segmentation of normalized log2 ratios (specifically, log2(CN/2)) was performed using the circular binary segmentation (CBS) algorithm.

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mRNA expression  (8.0GB) Gene expression  (Published) 

Affymetrix U133+2 arrays.
Raw Affymetrix CEL files were converted to a single value for each probe set using Robust Multi-array Average (RMA) and normalized using quantile normalization. Either the original Affymetrix U133+2 CDF file or a redefined custom CDF file (ENTREZG - v15) was used for the summarization.

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Cell Line Annotations  (196.1KB) Sample annotation  (Published) 

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Oncomap mutations  (464.8KB) Mutation  (Published) 

Oncomap mutation data.
The mutations were assessed in 33 genes (381 specific mutations) using Oncomap 3.0 core. See the associated publication.

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Hybrid capture sequencing  (6.5GB) Mutation  (In process) 

List of mutations and indels in 1651 genes, determined by targeted massively parallel sequencing. Note: the hybrid capture process might yield sequences in genes outside of the target list; those were kept in the analysis and mutations in these genes are present in the files below.

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Pharmacological profiling  (8.0MB) Drug data  (Published) 

Pharmacologic profiles for 24 anticancer drugs across 504 cell lines.

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binary calls for copy number and mutation data   (95.9MB) Mutation  (In process) 

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